------------------------------------------------------------------------ r2076 | pemsley | 2009-06-19 18:34:57 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/src/c-interface.h Fix up function documentation. ------------------------------------------------------------------------ r2075 | pemsley | 2009-06-19 14:30:46 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/scheme/fitting.scm M /trunk/src/c-interface-gui.cc Tweak the sensitivities of the refinement buttons for better clarity. ------------------------------------------------------------------------ r2074 | pemsley | 2009-06-19 14:30:11 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New table. ------------------------------------------------------------------------ r2073 | pemsley | 2009-06-19 14:16:02 +0100 (Fri, 19 Jun 2009) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm More protection in residue-alt-confs, atom-ls might be #f from residue-info (if residue not found). ------------------------------------------------------------------------ r2072 | pemsley | 2009-06-19 13:58:56 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New annotation, extend the days. ------------------------------------------------------------------------ r2071 | pemsley | 2009-06-19 11:52:34 +0100 (Fri, 19 Jun 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/nsv.cc Actually move to the atom on a GDK_BUTTON_RELEASE, not a motion event. Fixed JED bug. ------------------------------------------------------------------------ r2070 | pemsley | 2009-06-19 00:29:11 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/generate-svn-revision-cc.sh Fix quoting problems in comment string. ------------------------------------------------------------------------ r2069 | pemsley | 2009-06-19 00:08:18 +0100 (Fri, 19 Jun 2009) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh Don't GLADE_HOOKUP_OBJECT() for model_toolbar_rot_trans_toolbutton when GTK_TYPE_MENU_TOOL_BUTTON not defined. Fixes CentOS 4.6 crash. ------------------------------------------------------------------------ r2068 | pemsley | 2009-06-19 00:07:00 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/generate-svn-revision-cc.sh update teh svn-revision.cc file, now we seem to need extern "C". ------------------------------------------------------------------------ r2067 | pemsley | 2009-06-19 00:05:56 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Updates for svn_revision() - formatting. ------------------------------------------------------------------------ r2066 | pemsley | 2009-06-18 13:44:03 +0100 (Thu, 18 Jun 2009) | 6 lines Changed paths: A /trunk/update-binary/check-for-updates.scm A /trunk/update-binary/download-binary-cmd.scm M /trunk/update-binary/phone-home.scm Updates for updating binaries. Tested on pre-release. GTK2+ only (because of threads). Now we call the sever and check the type-binary*latest.txt file to find the latest built version. The check-for-updates extension is not added in (as yet). ------------------------------------------------------------------------ r2065 | pemsley | 2009-06-17 12:07:03 +0100 (Wed, 17 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple fix typo. ------------------------------------------------------------------------ r2064 | b.lohkamp | 2009-06-17 11:04:27 +0100 (Wed, 17 Jun 2009) | 3 lines Changed paths: M /trunk/doc/tutorial-2.tex M /trunk/doc/tutorial.tex M /trunk/python-tests/02_shelx.py M /trunk/python-tests/07_ncs.py update tutorials add some imol tests/protection to some python tests ------------------------------------------------------------------------ r2063 | pemsley | 2009-06-17 10:19:54 +0100 (Wed, 17 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Experimental latest build for binary type text file added. ------------------------------------------------------------------------ r2062 | pemsley | 2009-06-16 18:51:23 +0100 (Tue, 16 Jun 2009) | 4 lines Changed paths: M /trunk/README M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/gtk2-interface.c Add protection for looking up sequence_view_dialog [Fixes crash]. Also lookup nsv_dialog. Resize the buttons on the preferences dialog. ------------------------------------------------------------------------ r2061 | pemsley | 2009-06-16 18:38:20 +0100 (Tue, 16 Jun 2009) | 2 lines Changed paths: M /trunk/src/nsv.cc Use an int for looping over residue number ticks (not unsigned int). ------------------------------------------------------------------------ r2060 | pemsley | 2009-06-14 23:29:21 +0100 (Sun, 14 Jun 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/fitting.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add in coot-sys-build-type function (scheme only so far). Use -DCOOT_SYS_BUILD_TYPE in the src/Makefile.am. ------------------------------------------------------------------------ r2059 | pemsley | 2009-06-14 17:59:10 +0100 (Sun, 14 Jun 2009) | 3 lines Changed paths: A /trunk/update-binary A /trunk/update-binary/notes A /trunk/update-binary/phone-home.scm Add some test/play code for seeing what binaries are available on the web site. Somehow report back to user for update/download/install. ------------------------------------------------------------------------ r2058 | pemsley | 2009-06-14 01:06:32 +0100 (Sun, 14 Jun 2009) | 2 lines Changed paths: M /trunk/macros/sys-build-type.m4 Tweak the COOT_SYS_BUILD_TYPE into shape. Not yet used in src/Makefile.am ------------------------------------------------------------------------ r2057 | pemsley | 2009-06-14 00:41:36 +0100 (Sun, 14 Jun 2009) | 3 lines Changed paths: M /trunk/configure.in A /trunk/macros/sys-build-type.m4 Start to add sys build type into build system - to be used by updating-binaries mechanism. ------------------------------------------------------------------------ r2056 | pemsley | 2009-06-13 01:11:34 +0100 (Sat, 13 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add coot revision info to build status line. ------------------------------------------------------------------------ r2055 | pemsley | 2009-06-12 08:51:50 +0100 (Fri, 12 Jun 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c Delete unused declaration of a GFile in on_coords_filechooserdialog1_response(). ------------------------------------------------------------------------ r2054 | pemsley | 2009-06-12 02:49:22 +0100 (Fri, 12 Jun 2009) | 4 lines Changed paths: M /trunk/src/callbacks.c gtk_file_chooser_get_files() is too modern for old GTK2s. So use gtk_file_chooser_get_filenames(), which returns a GSList of char * filenames (not GFiles). ------------------------------------------------------------------------ r2053 | pemsley | 2009-06-11 17:21:06 +0100 (Thu, 11 Jun 2009) | 3 lines Changed paths: M /trunk/src/callbacks.c GTK1 doesn't have gtk_file_selection_get_selections, so ifdef it out and use the old (singl) file mechanism for GTK1. ------------------------------------------------------------------------ r2052 | pemsley | 2009-06-11 14:18:22 +0100 (Thu, 11 Jun 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/globjects.cc Shift-click and ctrl-click enabled in reading coordinate files by using gtk_file_chooser_get_files() etc. ------------------------------------------------------------------------ r2051 | b.lohkamp | 2009-06-09 22:37:43 +0100 (Tue, 09 Jun 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py add python test for refinement with zero bond esd ------------------------------------------------------------------------ r2050 | pemsley | 2009-06-09 17:50:30 +0100 (Tue, 09 Jun 2009) | 5 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Add a Cancel button to multi-refine button set. Pressing the stop button makes the Cancel button visible Pressing the stop button makes the Cancel button sensitive. Pressing the continue button makes the Cancel button insensitive. ------------------------------------------------------------------------ r2049 | pemsley | 2009-06-08 14:19:53 +0100 (Mon, 08 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New annotation on burn-up graph. ------------------------------------------------------------------------ r2048 | b.lohkamp | 2009-06-08 07:25:30 +0100 (Mon, 08 Jun 2009) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fix typo in new TER test ------------------------------------------------------------------------ r2047 | b.lohkamp | 2009-06-07 22:58:31 +0100 (Sun, 07 Jun 2009) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/scheme/extensions.scm add 3D annotations for python update some python tests (TER on water chain...) ------------------------------------------------------------------------ r2046 | pemsley | 2009-06-07 16:20:19 +0100 (Sun, 07 Jun 2009) | 2 lines Changed paths: M /trunk/build/CalphaBuild.cc M /trunk/build/CalphaBuild.hh M /trunk/build/Makefile.am M /trunk/build/testcabuild.cc M /trunk/burn-up/new-graph.py M /trunk/coords/Bond_lines.h M /trunk/coords/Bond_lines_ext.cc M /trunk/coords/Cartesian.cc M /trunk/coords/Cartesian.h M /trunk/coords/Makefile.am M /trunk/coords/coot-close.cc M /trunk/coords/cos-sin.cc M /trunk/coords/cos-sin.h M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-crystal.h M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/coords/utils.cc M /trunk/coords/utils.h M /trunk/coot-surface/Makefile.am M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/atomic-numbers.cc M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-fasta.cc M /trunk/coot-utils/coot-fasta.hh M /trunk/coot-utils/coot-fffear.cc M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-shelx.hh M /trunk/coot-utils/coot-trim.hh M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/coot-utils/test-shelx-reader.cc M /trunk/coot-utils/test-utils.cc M /trunk/coot-utils/trim.cc M /trunk/cootaneer/Makefile.am M /trunk/db-main/db-main.hh M /trunk/db-main/db-strands.cc M /trunk/db-main/db-strands.hh M /trunk/density-contour/Makefile.am M /trunk/geometry/Makefile.am M /trunk/geometry/Makefile.simple M /trunk/geometry/protein-geometry-mmdb.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/test-geometry.cc M /trunk/high-res/Makefile.am M /trunk/high-res/coot-atom-graph.cc M /trunk/high-res/coot-atom-graph.hh M /trunk/high-res/coot-node-info.hh M /trunk/high-res/globularize.cc M /trunk/high-res/high-res.cc M /trunk/high-res/residue-distortions.cc M /trunk/high-res/sequence-assignment.cc M /trunk/high-res/sequence-assignment.hh M /trunk/high-res/test-atom-graph.cc M /trunk/high-res/testseqalign.cc M /trunk/high-res/testseqassignment.cc M /trunk/high-res/trace-high-res.cc M /trunk/ideal/Makefile.simple M /trunk/ideal/lograma.h M /trunk/ideal/molmantest.cc M /trunk/ideal/pepflip.cc M /trunk/ideal/pepflip.hh M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/regularize-minimol.hh M /trunk/ideal/test-indexing.cc M /trunk/ideal/test-indexing.hh M /trunk/ideal/with-geometry.cc M /trunk/ligand/Makefile.am M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/ligand/dunbrack.cc M /trunk/ligand/dunbrack.hh M /trunk/ligand/fast-ss-search.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.hh M /trunk/ligand/monomer-utils.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/residue_by_phi_psi.cc M /trunk/ligand/residue_by_phi_psi.hh M /trunk/ligand/rigid-body.cc M /trunk/ligand/rigid-body.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-fffear-in-coot.cc M /trunk/ligand/test-helix-placement.cc M /trunk/ligand/test-random.cc M /trunk/ligand/testdunbrack.cc M /trunk/macros/Makefile.am M /trunk/macros/clipper.m4 M /trunk/macros/coot-database.m4 M /trunk/macros/coot-windows.m4 M /trunk/macros/glut.m4 M /trunk/macros/guile-gtk.m4 M /trunk/macros/mmdb-ssm.m4 M /trunk/macros/mmdb.m4 M /trunk/macros/with-guile.m4 M /trunk/mini-mol/Makefile.am M /trunk/mini-mol/mini-mol-utils.cc M /trunk/mini-mol/mini-mol-utils.hh M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/mini-mol/testminimol.cc M /trunk/python/Makefile.am M /trunk/python/coot_lsq.py M /trunk/python/tips.py M /trunk/scheme/coot-lsq.scm M /trunk/scheme/coot.scm M /trunk/scheme/fitting.scm M /trunk/scheme/generic-objects.scm M /trunk/scheme/group-settings.scm M /trunk/scheme/mutate.scm M /trunk/scheme/refmac.scm M /trunk/scheme/tips-gui.scm M /trunk/sequence-view/Makefile.am M /trunk/sequence-view/sequence-view.cc M /trunk/sequence-view/sequence-view.hh M /trunk/setup/coot.csh.in M /trunk/setup/coot.sh.in M /trunk/skeleton/BuildCas.cc M /trunk/skeleton/Makefile.am M /trunk/src/c-inner-main.c M /trunk/src/c-interface.h M /trunk/src/callbacks.h M /trunk/src/coot_pythonmodule.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info-widget-work.cc M /trunk/src/pick.cc M /trunk/src/positioned-widgets.h M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh M /trunk/src/read-phs.c M /trunk/src/read-phs.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh M /trunk/surface/CXXChargeTable.cpp M /trunk/surface/CXXChargeTable.h M /trunk/surface/CXXCircle.cpp M /trunk/surface/CXXCircle.h M /trunk/surface/CXXCircleNode.cpp M /trunk/surface/CXXCircleNode.h M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCoord.h M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXCreator.h M /trunk/surface/CXXException.cpp M /trunk/surface/CXXException.h M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXFFTSolventMap.h M /trunk/surface/CXXFortranFile.cpp M /trunk/surface/CXXFortranFile.h M /trunk/surface/CXXMatrix4x4.h M /trunk/surface/CXXNewHood.cpp M /trunk/surface/CXXNewHood.h M /trunk/surface/CXXNode.cpp M /trunk/surface/CXXNode.h M /trunk/surface/CXXPointyBit.h M /trunk/surface/CXXQADSurface.cpp M /trunk/surface/CXXQADSurface.h M /trunk/surface/CXXQADSurfaceStaticData.cpp M /trunk/surface/CXXSpace.cpp M /trunk/surface/CXXSpace.h M /trunk/surface/CXXSphereElement.cpp M /trunk/surface/CXXSphereElement.h M /trunk/surface/CXXSphereFlatTriangle.h M /trunk/surface/CXXSphereNode.cpp M /trunk/surface/CXXSphereNode.h M /trunk/surface/CXXSphereTriangle.cpp M /trunk/surface/CXXSphereTriangle.h M /trunk/surface/CXXSphereTriangleEdge.cpp M /trunk/surface/CXXSphereTriangleEdge.h M /trunk/surface/CXXSurface.cpp M /trunk/surface/CXXSurface.h M /trunk/surface/CXXSurfaceVertex.cpp M /trunk/surface/CXXSurfaceVertex.h M /trunk/surface/CXXTorusElement.cpp M /trunk/surface/CXXTorusElement.h M /trunk/surface/CXXTorusNode.cpp M /trunk/surface/CXXTorusNode.h M /trunk/surface/CXXTorusTriangle.cpp M /trunk/surface/CXXTorusTriangle.h M /trunk/surface/CXXTorusTriangle.h.h M /trunk/surface/CXXTriangle.cpp M /trunk/surface/CXXTriangle.h M /trunk/surface/CXXUtils.cpp M /trunk/surface/CXXUtils.h M /trunk/surface/ElectroSurface.cpp M /trunk/surface/TokenIterator.h M /trunk/surface/surface.cpp M /trunk/surface/surface.h M /trunk/tw/Makefile.am M /trunk/tw/coot-tw.hh M /trunk/tw/cootsound.c Make the license clearly version 3. ------------------------------------------------------------------------ r2045 | pemsley | 2009-06-07 13:59:14 +0100 (Sun, 07 Jun 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Move "set spin speed" into setttings in Extensions. ------------------------------------------------------------------------ r2044 | pemsley | 2009-06-06 19:03:41 +0100 (Sat, 06 Jun 2009) | 4 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add the "3D annotations" (just the same as we did on the mailing list several weeks ago). Under Extensions -> Representations. Scheme only so far. Add documentation for this. ------------------------------------------------------------------------ r2043 | pemsley | 2009-06-04 21:25:06 +0100 (Thu, 04 Jun 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add protection for NULL residues and chains in construct_from_model_links(). ------------------------------------------------------------------------ r2042 | pemsley | 2009-06-04 16:08:10 +0100 (Thu, 04 Jun 2009) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/ideal/simple-restraint.cc Add long bonds for element AU. Bond limit is 2.4 for AU. Rework debugging of bond restraints - easier for next time. ------------------------------------------------------------------------ r2041 | pemsley | 2009-06-04 01:00:21 +0100 (Thu, 04 Jun 2009) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Additional niceness on the map sharpening slider. ("Sharpen" and "blur" are offset down a line). ------------------------------------------------------------------------ r2040 | pemsley | 2009-06-03 23:32:09 +0100 (Wed, 03 Jun 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/doc/tutorial.tex M /trunk/src/c-interface-gui.cc M /trunk/src/gtk2-interface.c Tweak the scale for sharpening, how the marks work properly. ------------------------------------------------------------------------ r2039 | pemsley | 2009-06-03 23:17:16 +0100 (Wed, 03 Jun 2009) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix typo, add extra markup arg for gtk_scale_add_mark(). ------------------------------------------------------------------------ r2038 | pemsley | 2009-06-03 22:39:06 +0100 (Wed, 03 Jun 2009) | 10 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/rotamer.cc M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h TER record on water chain is correctly removed now. Add test for this. On save coords, the active item is from the first molecule with unsaved changes. When refining, check for single HETATM atom in residue, if so, refine with rigid body. Water addtion add HETATMs. Residue names corrected for BR, CA, NA, CL, MG. TER waters are not used in water validation tests. 1 and 999 are added into the residue number entries in the LSQ fit dialog. ------------------------------------------------------------------------ r2037 | pemsley | 2009-06-02 02:28:16 +0100 (Tue, 02 Jun 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add TER atom protection for second atom in LINK too. ------------------------------------------------------------------------ r2036 | pemsley | 2009-06-02 02:25:49 +0100 (Tue, 02 Jun 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add TER atom protection in construct_from_model_links(). ------------------------------------------------------------------------ r2035 | pemsley | 2009-06-01 02:08:52 +0100 (Mon, 01 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New limits for burn-up graph. ------------------------------------------------------------------------ r2034 | pemsley | 2009-06-01 02:06:53 +0100 (Mon, 01 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fixups for build log redirection. ------------------------------------------------------------------------ r2033 | pemsley | 2009-05-31 15:07:36 +0100 (Sun, 31 May 2009) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/cc-interface.hh Handle esd of 0 in restraints. Add a test for esd of 0 in restraints. Reformat for doxygen documentation of monomer functions. ------------------------------------------------------------------------ r2032 | pemsley | 2009-05-30 15:36:55 +0100 (Sat, 30 May 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info.cc Remove debugging. ------------------------------------------------------------------------ r2031 | pemsley | 2009-05-30 15:36:14 +0100 (Sat, 30 May 2009) | 2 lines Changed paths: M /trunk/scheme/gap.scm Fix for rama restraints usage in fit-gap. ------------------------------------------------------------------------ r2030 | pemsley | 2009-05-30 15:32:09 +0100 (Sat, 30 May 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Add bonds for link entities (construct_from_model_link()). ------------------------------------------------------------------------ r2029 | b.lohkamp | 2009-05-29 15:58:17 +0100 (Fri, 29 May 2009) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h enable Zalman stereo mode (for testing) Add build info to mmdb and clipper logs (windows). ------------------------------------------------------------------------ r2028 | b.lohkamp | 2009-05-27 10:25:34 +0100 (Wed, 27 May 2009) | 1 line Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm remove sharpen map from Extensions (py and scm) ------------------------------------------------------------------------ r2027 | pemsley | 2009-05-26 00:27:58 +0100 (Tue, 26 May 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h Put the Sharpening GUI in the Calculate menu. There it will have tick marks if GTK+ version is recent enough. ------------------------------------------------------------------------ r2026 | pemsley | 2009-05-24 10:12:11 +0100 (Sun, 24 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add build info to mmdb and clipper logs. ------------------------------------------------------------------------ r2025 | pemsley | 2009-05-23 07:46:20 +0100 (Sat, 23 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update to guile-1.8.6 ------------------------------------------------------------------------ r2024 | b.lohkamp | 2009-05-22 18:19:01 +0100 (Fri, 22 May 2009) | 1 line Changed paths: M /trunk/configure.in M /trunk/macros/clipper.m4 M /trunk/src/c-interface-gui.cc check for new clipper in configure ------------------------------------------------------------------------ r2023 | b.lohkamp | 2009-05-22 16:57:40 +0100 (Fri, 22 May 2009) | 4 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc update to new clipper 2.1 090520 fix real exit on windows (with help of new clipper) update sharpen map GUI ------------------------------------------------------------------------ r2022 | pemsley | 2009-05-22 06:46:37 +0100 (Fri, 22 May 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi The command to return the symmetry is get-symmetry, not show-symmetry. ------------------------------------------------------------------------ r2021 | pemsley | 2009-05-18 13:29:54 +0100 (Mon, 18 May 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/scheme/coot-gui.scm Hack out several items in the todo list for the next release. Adjust the sharpening gui slightly. ------------------------------------------------------------------------ r2020 | b.lohkamp | 2009-05-17 21:39:57 +0100 (Sun, 17 May 2009) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface.h fix python tests is_shelx_molecule for all (not just GUILE) ------------------------------------------------------------------------ r2019 | b.lohkamp | 2009-05-17 17:27:42 +0100 (Sun, 17 May 2009) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/begin.py M /trunk/src/c-interface-preferences.cc add python scripting functions for sharpening maps update python shelx tests ------------------------------------------------------------------------ r2018 | b.lohkamp | 2009-05-17 14:39:02 +0100 (Sun, 17 May 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python/shelx.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/begin.py fix startup with toolbuttons (quick hack) add nomenclature errors to python extensions get_atom in python tests take ins-code now add python test for alt conf pepflip ------------------------------------------------------------------------ r2017 | pemsley | 2009-05-17 13:09:48 +0100 (Sun, 17 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove more >&2s. ------------------------------------------------------------------------ r2016 | pemsley | 2009-05-17 12:20:06 +0100 (Sun, 17 May 2009) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Remove addition standard error build logging because bragg3 choked on it (for some reason). ------------------------------------------------------------------------ r2015 | pemsley | 2009-05-15 13:50:46 +0100 (Fri, 15 May 2009) | 7 lines Changed paths: M /trunk/TODO M /trunk/greg-tests/02-shelx.scm M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add Map Sharpening GUI. Add shelx occupancy on terminal residue addition test. Add a optional arg to install_model() and use it to pass shelx molecule state. Rename multi-fit menu items. Add shelx-molecule? to scheme functions Add shelx molecule flag inheritance test. ------------------------------------------------------------------------ r2014 | kevin.cowtan | 2009-05-15 13:50:24 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix CNS code so it actually works. ------------------------------------------------------------------------ r2013 | kevin.cowtan | 2009-05-15 12:20:00 +0100 (Fri, 15 May 2009) | 4 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Actually turn on data of fphidata for some of the input modes. Still expect sharpen() to crash when using other input types. ------------------------------------------------------------------------ r2012 | kevin.cowtan | 2009-05-15 10:41:52 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix up make_map_from_mtz_by_calc_phases. ------------------------------------------------------------------------ r2011 | kevin.cowtan | 2009-05-15 10:38:06 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix sharpen to use clipper2-style HKL_data initialisation. ------------------------------------------------------------------------ r2010 | kevin.cowtan | 2009-05-15 10:33:52 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix CNS read to work with new sharpen function too. (hopefully) ------------------------------------------------------------------------ r2009 | kevin.cowtan | 2009-05-15 10:22:05 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h [CLIPPER2 CLEANUP] Rewrite calculate_sfs_and_make_map to remove HKL_info from API. ------------------------------------------------------------------------ r2008 | pemsley | 2009-05-14 19:31:33 +0100 (Thu, 14 May 2009) | 4 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Add Kevin's patch so that sharpen() works using the original data. The 2 fft method was scrapped. This method is more complex and invasive to other functions. ------------------------------------------------------------------------ r2007 | pemsley | 2009-05-14 19:25:52 +0100 (Thu, 14 May 2009) | 2 lines Changed paths: M /trunk/src/c-interface.h Fix up function descriptions for better doxygenation. ------------------------------------------------------------------------ r2006 | pemsley | 2009-05-14 15:19:00 +0100 (Thu, 14 May 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Fix typo in debugging line. ------------------------------------------------------------------------ r2005 | pemsley | 2009-05-14 13:19:55 +0100 (Thu, 14 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Rework the sharpen function - now does a 2-way (back and forwards) transform based on the map (not original Fphis). needs more work yet. ------------------------------------------------------------------------ r2004 | pemsley | 2009-05-14 00:51:55 +0100 (Thu, 14 May 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/doc/tutorial.tex M /trunk/geometry/protein-geometry.cc M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/gtk2-interface.c Add icon and change text for Display Manager "close" button. check the three-letter-code for restraints in chiral volume analysis. Add the toolbar_multi_refine buttons which seem to have been lost. Remove some debugging. ------------------------------------------------------------------------ r2003 | pemsley | 2009-05-12 16:38:08 +0100 (Tue, 12 May 2009) | 5 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Make the "whole molecule" fitting functions interruptible. Introduce Stop and Continue buttons to the toolbar (they don't take focus). on_toolbar_multi_refine_continue_button_clicked() and on_toolbar_multi_refine_stop_button_clicked() callbacks added. ------------------------------------------------------------------------ r2002 | b.lohkamp | 2009-05-11 14:45:48 +0100 (Mon, 11 May 2009) | 1 line Changed paths: M /trunk/src/c-interface-mmdb.cc add the optional argument in python expression (forgot in last commit) ------------------------------------------------------------------------ r2001 | b.lohkamp | 2009-05-11 14:44:50 +0100 (Mon, 11 May 2009) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/extensions.py M /trunk/python/shelx_extensions.py M /trunk/python/unittest_extensions.py M /trunk/python-tests/01_pdb_mtz.py add merge_solvent_chains to extensions add test for DNA mutate and merge_solvent_chains fix new test for pepflip (using alt_conf now) Add an optional argument to the occ_b_ele list, in interpretation of a python representation of a molecule that is the segid. python shelx refine work via editable gui with and without given HKL filename ------------------------------------------------------------------------ r2000 | pemsley | 2009-05-11 14:16:22 +0100 (Mon, 11 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Fix Tim Grune bug - shelx molecules should honour the "don't recentre" option-menu. ------------------------------------------------------------------------ r1999 | pemsley | 2009-05-11 13:29:17 +0100 (Mon, 11 May 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-utils.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/begin.grg M /trunk/ideal/pepflip.cc M /trunk/ideal/pepflip.hh M /trunk/python/fitting.py M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Re-write of pepflip (Ingo Korndoefer bug). pepflip now takes an insertion-code argument. get-atom now takes an insertion-code argument. Fix Nomenclature errors is added to Extensions. next_residue() and previous_residue() util functions introduced. ------------------------------------------------------------------------ r1998 | b.lohkamp | 2009-05-10 22:33:25 +0100 (Sun, 10 May 2009) | 1 line Changed paths: M /trunk/build-it-win update WinCoot to mmdb-1.21 ------------------------------------------------------------------------ r1997 | pemsley | 2009-05-09 12:11:47 +0100 (Sat, 09 May 2009) | 2 lines Changed paths: M /trunk/TODO A /trunk/doc/c-interface_8h.texi M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/callbacks.c Include the doxygen->xml->texi documentation for c-interface functions. ------------------------------------------------------------------------ r1996 | pemsley | 2009-05-09 11:13:27 +0100 (Sat, 09 May 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi User manual now includes c-interface_8h.texi ------------------------------------------------------------------------ r1995 | pemsley | 2009-05-09 00:32:21 +0100 (Sat, 09 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple protect $update_libtool usage. ------------------------------------------------------------------------ r1994 | pemsley | 2009-05-08 17:33:29 +0100 (Fri, 08 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/gtk-manual.cc Don't look for non-existent map_scroll_buttons in get_radio_button_in_scroll_group(). ------------------------------------------------------------------------ r1993 | pemsley | 2009-05-08 14:47:32 +0100 (Fri, 08 May 2009) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/support.c M /trunk/src/support.h Add a destroy callback for the symmetry_controller_dialog. Use it to make just one instance of the symmetry_controller_dialog. Guile version fixes in src/c-interface-mmdb.cc. ------------------------------------------------------------------------ r1992 | pemsley | 2009-05-08 13:56:47 +0100 (Fri, 08 May 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/src/graphics-info-state.cc Don't save a state file on exit if started with --nos-state-script. ------------------------------------------------------------------------ r1991 | pemsley | 2009-05-08 08:59:48 +0100 (Fri, 08 May 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/Makefile.am add density-score-by-residue to dist_bin_SCRIPTS ------------------------------------------------------------------------ r1990 | pemsley | 2009-05-08 08:55:43 +0100 (Fri, 08 May 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix up build-script post-install-slim to account for density-score-by-residue. ------------------------------------------------------------------------ r1989 | pemsley | 2009-05-08 08:53:58 +0100 (Fri, 08 May 2009) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo M /trunk/src/Makefile.am A /trunk/src/density-score-by-residue Put density-score-by-residue in the tarball, so we need a density-score-by-residue-real. ------------------------------------------------------------------------ r1988 | pemsley | 2009-05-07 23:22:49 +0100 (Thu, 07 May 2009) | 5 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add an optional argument to the occ_b_ele list, in interpretation of a scheme representation of a molecule that is the segid. Add Torsion general to docs. New Y range for burnup graph. ------------------------------------------------------------------------ r1987 | pemsley | 2009-05-07 20:51:11 +0100 (Thu, 07 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface.cc Reading a CCP4 map no longer leaves the Display Control scroll button in an inconsistent state (JED bug). ------------------------------------------------------------------------ r1986 | pemsley | 2009-05-07 14:20:28 +0100 (Thu, 07 May 2009) | 4 lines Changed paths: M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Change seqDist to 0 (work around mmdb bug/strangeness) in SeekContacts() for environment distances - fixes Steven Sheriff bug. Delete the atom selection in make_environment_bonds_box() fixes a memory leak. ------------------------------------------------------------------------ r1985 | pemsley | 2009-05-07 10:27:09 +0100 (Thu, 07 May 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h Add a dashed line interface to generic objects. ------------------------------------------------------------------------ r1984 | pemsley | 2009-05-06 23:08:55 +0100 (Wed, 06 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/nsv.cc M /trunk/src/nsv.hh Adjustments to the new sequence view. Handle residue number offsets, so that the ticks, axes, letter no longer appear far to the right. ------------------------------------------------------------------------ r1983 | pemsley | 2009-05-06 22:24:52 +0100 (Wed, 06 May 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Days range to 160 ------------------------------------------------------------------------ r1982 | pemsley | 2009-05-06 18:23:12 +0100 (Wed, 06 May 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/rel-todo Upgrade build scripts to use mmdb 1.21. ------------------------------------------------------------------------ r1981 | pemsley | 2009-05-06 18:17:00 +0100 (Wed, 06 May 2009) | 2 lines Changed paths: M /trunk/scheme/shelx-extensions.scm Make SHELXL refine work via editable gui with and without given HKL filename. ------------------------------------------------------------------------ r1980 | pemsley | 2009-05-06 17:35:24 +0100 (Wed, 06 May 2009) | 6 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/peak-search.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/happy-coot-diary.html M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Add merge-solvent-chains function, with GUI and test. Add DNA mutation test. add background_is_black_p() to graphics-info class. And use it in draw_anti_aliasing(). More additions to rel-todo and TODO. ------------------------------------------------------------------------ r1979 | b.lohkamp | 2009-05-05 13:09:48 +0100 (Tue, 05 May 2009) | 6 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/generic_objects.py M /trunk/python/shelx.py M /trunk/python/shelx_extensions.py A /trunk/python/test_internal.py M /trunk/python/tips.py update python scripts: - fix typos and update tips - fix shelxl refine and reading of lst file - add probe_local_sphere - add simple test_internal script ------------------------------------------------------------------------ r1978 | pemsley | 2009-05-05 12:28:44 +0100 (Tue, 05 May 2009) | 3 lines Changed paths: M /trunk/rel-todo A /trunk/scheme/test-internal.scm Add simple test-internal script to run the internal tests and exit appropriately. ------------------------------------------------------------------------ r1977 | pemsley | 2009-05-02 00:01:12 +0100 (Sat, 02 May 2009) | 3 lines Changed paths: M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/dnotes M /trunk/ligand/chi-angles.cc M /trunk/rel-todo M /trunk/scheme/remote-control.scm M /trunk/src/testing.cc M /trunk/src/testing.hh Add a function to limit the peak search so that smaller peaks are not listed if a bigger one (absolute) is nearby. ------------------------------------------------------------------------ r1976 | pemsley | 2009-05-01 11:02:37 +0100 (Fri, 01 May 2009) | 4 lines Changed paths: M /trunk/scheme/generic-objects.scm M /trunk/scheme/shelx-extensions.scm M /trunk/scheme/shelx.scm Fix up problem in shelx refine [Tobias Beck]. New molecules by atom selection created as part of probe-local-sphere should not be active. ------------------------------------------------------------------------ r1975 | pemsley | 2009-05-01 10:42:11 +0100 (Fri, 01 May 2009) | 2 lines Changed paths: A /trunk/doc/interface-xml-to-texi.xsl M /trunk/doc/user-manual.texi Add xslt filter for c-interface.h xml doxygen docs to texi. ------------------------------------------------------------------------ r1974 | pemsley | 2009-04-30 17:47:31 +0100 (Thu, 30 Apr 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New limits for graph. ------------------------------------------------------------------------ r1973 | pemsley | 2009-04-29 18:28:58 +0100 (Wed, 29 Apr 2009) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Make glycosidic bond debugging conditional. ------------------------------------------------------------------------ r1972 | pemsley | 2009-04-29 18:09:57 +0100 (Wed, 29 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo. ------------------------------------------------------------------------ r1971 | pemsley | 2009-04-29 17:08:19 +0100 (Wed, 29 Apr 2009) | 2 lines Changed paths: M /trunk/src/coot.in unexport LANG, LC_ALL, LC_NUMERIC. ------------------------------------------------------------------------ r1970 | pemsley | 2009-04-28 22:27:41 +0100 (Tue, 28 Apr 2009) | 2 lines Changed paths: M /trunk/scheme/tips.scm Fix some typos, clarify. ------------------------------------------------------------------------ r1969 | pemsley | 2009-04-28 22:27:08 +0100 (Tue, 28 Apr 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py new graph annotations. ------------------------------------------------------------------------ r1968 | b.lohkamp | 2009-04-27 15:10:41 +0100 (Mon, 27 Apr 2009) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface.cc M /trunk/src/coot.i M /trunk/src/graphics-info.cc bug fix protein refinemetn options in extensions dont export main_widgets to python (actually should do same for all proper GTK widgets!?) fix reference counting for safe_python_with_return (should fix Ramachandran/ post_manipulation_hook_py problems - finally) add test for post_manipulation_hook_py/Ramachandran ------------------------------------------------------------------------ r1967 | pemsley | 2009-04-27 12:26:25 +0100 (Mon, 27 Apr 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Remove python and its config from bin in slimmed dir. ------------------------------------------------------------------------ r1966 | pemsley | 2009-04-27 11:14:04 +0100 (Mon, 27 Apr 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc Convert samplings to ints in reinterp_map_fine_gridding(). ------------------------------------------------------------------------ r1965 | pemsley | 2009-04-25 11:42:12 +0100 (Sat, 25 Apr 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/testing.cc Fix typo in util function canonical_base_name(). Use coot::util::nucleotide_is_DNA(r) in do_base_mutation(). (These 2 together fix bug when trying to mutate DNA). Fix limit check when adding view description (fixes esoteric crash). Fix typo in greg test name. ------------------------------------------------------------------------ r1964 | pemsley | 2009-04-24 14:15:08 +0100 (Fri, 24 Apr 2009) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Fix up typo in snarf-coot-docs ------------------------------------------------------------------------ r1963 | pemsley | 2009-04-24 08:47:55 +0100 (Fri, 24 Apr 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Add PYTHONPATH fix to gtk1 build version. ------------------------------------------------------------------------ r1962 | pemsley | 2009-04-23 11:20:57 +0100 (Thu, 23 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple set up PYTHONPATH when doing greg tests. ------------------------------------------------------------------------ r1961 | pemsley | 2009-04-23 10:33:59 +0100 (Thu, 23 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add diagnostics for test failure. ------------------------------------------------------------------------ r1960 | pemsley | 2009-04-22 23:24:25 +0100 (Wed, 22 Apr 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh Changes for improving the flooding by changing the gridding and giving user control to the atom mask radius and sigma level for a map. ------------------------------------------------------------------------ r1959 | pemsley | 2009-04-22 23:22:51 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1958 | pemsley | 2009-04-22 23:19:23 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New graph. ------------------------------------------------------------------------ r1957 | pemsley | 2009-04-22 19:01:46 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/rel-todo update todo list. ------------------------------------------------------------------------ r1956 | pemsley | 2009-04-22 18:59:47 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/src/coot-render.hh M /trunk/src/graphics-info-render.cc Some updates for renderman output. ------------------------------------------------------------------------ r1955 | pemsley | 2009-04-22 18:22:21 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Pipe std error to python test log too. ------------------------------------------------------------------------ r1954 | pemsley | 2009-04-22 18:20:17 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Fix typo. ------------------------------------------------------------------------ r1953 | b.lohkamp | 2009-04-22 11:25:41 +0100 (Wed, 22 Apr 2009) | 1 line Changed paths: M /trunk/src/c-interface.cc fix typo in safe_python_command_with_return ------------------------------------------------------------------------ r1952 | b.lohkamp | 2009-04-22 09:44:13 +0100 (Wed, 22 Apr 2009) | 1 line Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-it-win fix python auto-build testing, incl. PYTONHOME and PYTHONPATH ------------------------------------------------------------------------ r1951 | b.lohkamp | 2009-04-21 12:05:57 +0100 (Tue, 21 Apr 2009) | 5 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot.in M /trunk/src/main.cc import coot.py now move coot's python dir before global PYTHONPATH make safe_python_command_with_return failsafe if globals are not available (should fix errors related to post_manipulation_hook_py) ------------------------------------------------------------------------ r1947 | b.lohkamp | 2009-04-09 09:02:02 +0100 (Thu, 09 Apr 2009) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/src/graphics-info.cc fix python post_manipulation_hook and get_refmac_version ------------------------------------------------------------------------ r1946 | pemsley | 2009-04-03 10:51:51 +0100 (Fri, 03 Apr 2009) | 2 lines Changed paths: M /trunk/rel-todo Add new issues. ------------------------------------------------------------------------ r1945 | b.lohkamp | 2009-04-02 13:50:42 +0100 (Thu, 02 Apr 2009) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/scheme/coot-utils.scm M /trunk/src/graphics-info.cc fix run_post_manipulation_hook_py ------------------------------------------------------------------------ r1944 | pemsley | 2009-03-31 08:49:52 +0100 (Tue, 31 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Days to 110 ------------------------------------------------------------------------ r1943 | b.lohkamp | 2009-03-30 12:53:41 +0100 (Mon, 30 Mar 2009) | 1 line Changed paths: M /trunk/python/shelx.py fix import error ------------------------------------------------------------------------ r1942 | pemsley | 2009-03-30 12:25:48 +0100 (Mon, 30 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Tinker with the box placement. ------------------------------------------------------------------------ r1941 | pemsley | 2009-03-27 16:36:51 +0000 (Fri, 27 Mar 2009) | 2 lines Changed paths: M /trunk/dnotes Add ntoes. ------------------------------------------------------------------------ r1940 | b.lohkamp | 2009-03-27 15:36:46 +0000 (Fri, 27 Mar 2009) | 1 line Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/ideal/simple-restraint.cc M /trunk/src/graphics-info-modelling.cc revert alt conf refinement code back to revision 1933 ------------------------------------------------------------------------ r1939 | b.lohkamp | 2009-03-27 13:26:20 +0000 (Fri, 27 Mar 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/python/coot_utils.py M /trunk/python/shelx.py M /trunk/python/shelx_extensions.py fix and update shelx.py and shelx_extensions.py (now actually working, at least most of it, e.g. reading lst file and project) reading shelx ins file: treats tab as space now (was ignored before) and fix padding problem ------------------------------------------------------------------------ r1938 | pemsley | 2009-03-27 12:12:31 +0000 (Fri, 27 Mar 2009) | 3 lines Changed paths: M /trunk/src/testing.cc Find reference mtz file for test_ligand_fit_from_given_point() in ~/data/greg-data not . ------------------------------------------------------------------------ r1937 | pemsley | 2009-03-27 12:00:17 +0000 (Fri, 27 Mar 2009) | 5 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/src/c-interface.h Add a node for scripting functions in user-manual.texi Update doxygen name blocks in c-interface.h so that they do not clash with names from standard documentation. Update notes. ------------------------------------------------------------------------ r1936 | b.lohkamp | 2009-03-25 10:36:18 +0000 (Wed, 25 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/src/c-interface-preferences.cc M /trunk/src/callbacks.c fix question accept dialog order in preferences ------------------------------------------------------------------------ r1935 | b.lohkamp | 2009-03-23 15:32:13 +0000 (Mon, 23 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/src/graphics-info-gui.cc fix the reverse button show/hide for docked accept/reject dialog ------------------------------------------------------------------------ r1934 | b.lohkamp | 2009-03-23 15:05:26 +0000 (Mon, 23 Mar 2009) | 9 lines Changed paths: M /trunk/bldnotes M /trunk/coords/mmdb-extras.cc M /trunk/coot-gtk2.glade M /trunk/ideal/simple-restraint.cc M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/remote_control.py M /trunk/src/c-interface.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c enable reuse of python sockets enable refinement of multiple conformations (maybe should have a flag?!) no trafic lights for multiple residue refinement yet (if CA split)!? antialiasing depending on bg colour python GUI to find atoms with zero occ (needs scheme.guile version) reverse button for docked accept/refinement dialog (broken though as for normal accept/reject dialog...) ------------------------------------------------------------------------ r1933 | pemsley | 2009-03-23 10:03:32 +0000 (Mon, 23 Mar 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/cc-interface.hh More items in the todo list ------------------------------------------------------------------------ r1932 | pemsley | 2009-03-23 10:02:29 +0000 (Mon, 23 Mar 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm fix formatting of comments. ------------------------------------------------------------------------ r1931 | b.lohkamp | 2009-03-18 16:06:09 +0000 (Wed, 18 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py fixes for python SMILES GUI ------------------------------------------------------------------------ r1930 | b.lohkamp | 2009-03-17 16:56:25 +0000 (Tue, 17 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py fix for overwriting python key bindings ------------------------------------------------------------------------ r1929 | pemsley | 2009-03-17 00:43:07 +0000 (Tue, 17 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py X axis 100 days ------------------------------------------------------------------------ r1928 | pemsley | 2009-03-16 20:58:51 +0000 (Mon, 16 Mar 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix typo in smiles interface. Use label, not text. ------------------------------------------------------------------------ r1927 | pemsley | 2009-03-10 11:55:56 +0000 (Tue, 10 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Extra annotation for burn-up graph. ------------------------------------------------------------------------ r1926 | b.lohkamp | 2009-03-09 14:42:17 +0000 (Mon, 09 Mar 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/create_input_server.py M /trunk/python/create_server.py M /trunk/python/get_ebi.py M /trunk/python/remote_control.py update python scripts add python server control with timeout python threading only runs one timeout function and sleep time can be modified ------------------------------------------------------------------------ r1925 | pemsley | 2009-03-09 11:21:22 +0000 (Mon, 09 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Change day limit and ticks. ------------------------------------------------------------------------ r1924 | pemsley | 2009-03-06 17:59:09 +0000 (Fri, 06 Mar 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/get-ebi.scm M /trunk/scheme/remote-control.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/gtk2-interface.c Adjust remote-control a bit, now call pyrun-simple-string (a new function). End Transmission-string spelt correctly. And now ends in a newline char. Add function is-difference-map? Add pyrun_simple_string() scripting function. ------------------------------------------------------------------------ r1923 | pemsley | 2009-03-05 13:59:04 +0000 (Thu, 05 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Extend graph to 80 days. ------------------------------------------------------------------------ r1922 | pemsley | 2009-03-05 10:49:53 +0000 (Thu, 05 Mar 2009) | 2 lines Changed paths: M /trunk/rel-todo Update todo list. ------------------------------------------------------------------------ r1921 | pemsley | 2009-03-05 10:46:31 +0000 (Thu, 05 Mar 2009) | 2 lines Changed paths: M /trunk/rel-todo Update todo list. ------------------------------------------------------------------------ r1920 | pemsley | 2009-03-04 17:19:59 +0000 (Wed, 04 Mar 2009) | 2 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc Fix up problem when reverting wiggly-ligand.cc ------------------------------------------------------------------------ r1919 | pemsley | 2009-03-04 14:21:05 +0000 (Wed, 04 Mar 2009) | 4 lines Changed paths: M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/mgtree.h M /trunk/dnotes M /trunk/ligand/chi-angles.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/torsion-general.cc M /trunk/ligand/torsion-general.hh M /trunk/src/graphics-info-modelling.cc Revert back chi-angle/rotamer/mgtree code back to before 1877. (1877 to 1917 had broken chi angle code). Now this only has (again) broken wiggly ligand code. ------------------------------------------------------------------------ r1918 | b.lohkamp | 2009-03-04 13:28:19 +0000 (Wed, 04 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/coords/Bond_lines.cc quick fix for CA + ligand representation ------------------------------------------------------------------------ r1917 | b.lohkamp | 2009-03-03 22:39:41 +0000 (Tue, 03 Mar 2009) | 1 line Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in A /trunk/python/create_input_server.py A /trunk/python/create_server.py M /trunk/python/remote_control.py M /trunk/src/c-interface.cc some fixes and updates for python sockets ------------------------------------------------------------------------ r1916 | kevin.cowtan | 2009-03-03 14:24:50 +0000 (Tue, 03 Mar 2009) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add defines for secondard structure finding templates. Change the default for find_strands() to use latest best parameters. ------------------------------------------------------------------------ r1915 | b.lohkamp | 2009-03-03 11:02:22 +0000 (Tue, 03 Mar 2009) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/src/callbacks.c implement python threading with magic trickery (whats_new_dialog) ------------------------------------------------------------------------ r1914 | pemsley | 2009-03-02 10:55:15 +0000 (Mon, 02 Mar 2009) | 3 lines Changed paths: M /trunk/src/c-interface.h M /trunk/src/coot-dox.cfg Fix typo in doc string. Add xml output from doxygen. ------------------------------------------------------------------------ r1913 | pemsley | 2009-03-02 10:53:02 +0000 (Mon, 02 Mar 2009) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.6-pre-1.xpm Fix up missing pixels in splash screen. ------------------------------------------------------------------------ r1912 | b.lohkamp | 2009-03-01 22:10:21 +0000 (Sun, 01 Mar 2009) | 1 line Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/secondary-structure.svg M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h GUI for fast secondary structure search (GTK2) ------------------------------------------------------------------------ r1911 | kevin.cowtan | 2009-02-25 12:45:39 +0000 (Wed, 25 Feb 2009) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h New flexible secondary structure building code. ------------------------------------------------------------------------ r1910 | b.lohkamp | 2009-02-24 11:08:29 +0000 (Tue, 24 Feb 2009) | 1 line Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm add Find Secondary Structure in Extensions ------------------------------------------------------------------------ r1909 | pemsley | 2009-02-23 20:41:57 +0000 (Mon, 23 Feb 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Better debugging of sharpen(). ------------------------------------------------------------------------ r1908 | pemsley | 2009-02-23 19:16:47 +0000 (Mon, 23 Feb 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Remove debugging from map_fill_from_mtz_with_reso_limits(). ------------------------------------------------------------------------ r1907 | pemsley | 2009-02-23 19:15:34 +0000 (Mon, 23 Feb 2009) | 4 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Add the a container original_fphis after reading an MTZ file. Activate its use in sharpen - but that crashes currently. original_fphis have become invalid somehow. ------------------------------------------------------------------------ r1906 | b.lohkamp | 2009-02-23 13:45:06 +0000 (Mon, 23 Feb 2009) | 6 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python/unittest_extensions.py M /trunk/python-tests/begin.py M /trunk/src/molecule-class-info-maps.cc Python Extensions use sort_chains, not reorder_chains python dialog_box_with_buttonss can do HSep between buttons (use in unittest_extensions.py to separate tests belonging to different test classes) set_map_is_difference_map sets difference map colours and contour levels ------------------------------------------------------------------------ r1905 | pemsley | 2009-02-20 18:21:14 +0000 (Fri, 20 Feb 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix up guile-gui, post-neil-jerram patch added. ------------------------------------------------------------------------ r1904 | b.lohkamp | 2009-02-20 17:24:00 +0000 (Fri, 20 Feb 2009) | 1 line Changed paths: M /trunk/build-it-win some updates for windows autobuild ------------------------------------------------------------------------ r1903 | pemsley | 2009-02-20 13:04:52 +0000 (Fri, 20 Feb 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/scheme/extensions.scm Extensions use sort-chains, not reorder-chains. ------------------------------------------------------------------------ r1902 | b.lohkamp | 2009-02-19 15:05:12 +0000 (Thu, 19 Feb 2009) | 1 line Changed paths: M /trunk/python/generic_objects.py fix for pythonic interactive_probe ------------------------------------------------------------------------ r1901 | pemsley | 2009-02-19 14:54:14 +0000 (Thu, 19 Feb 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo M /trunk/src/Makefile.am A /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h Add more pisa interaction functions. A scripting interface - currently returns nothing. close_residues_from_different_molecules_t is a class because we need to handle the residue vectors before we trash the (combined) molecule. create_mmdbmanager_from_residue_vector() returns something sensible. ------------------------------------------------------------------------ r1900 | pemsley | 2009-02-19 10:16:26 +0000 (Thu, 19 Feb 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/happy-coot-diary.html M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/mol-hierachy.cc M /trunk/src/molecule-class-info.cc Add function new_molecule_by_symmetry(), where we give a fractional RTop. To coot-utils/coot-coord-utils.cc add function create_mmdbmanager_from_residue_vector() which will be used for creating models from symmetry/assembly interfaces. ------------------------------------------------------------------------ r1899 | pemsley | 2009-02-19 10:11:52 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix info output when building guile-lib. ------------------------------------------------------------------------ r1898 | pemsley | 2009-02-19 10:10:54 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/macros/glut.m4 Use $acl_libdirstem for glut macro. ------------------------------------------------------------------------ r1897 | pemsley | 2009-02-19 10:10:09 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/build-it Fix typo in outpu info when building guile-lib. ------------------------------------------------------------------------ r1896 | pemsley | 2009-02-19 09:52:54 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Fix crash when getting links from a CModel that is empty. ------------------------------------------------------------------------ r1895 | pemsley | 2009-02-18 20:44:45 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/rel-todo Add an item. ------------------------------------------------------------------------ r1894 | pemsley | 2009-02-18 16:19:18 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1893 | pemsley | 2009-02-18 13:59:04 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc Fix up shadow variable usage i in fill_chain_option_menu(). ------------------------------------------------------------------------ r1892 | pemsley | 2009-02-18 13:56:49 +0000 (Wed, 18 Feb 2009) | 3 lines Changed paths: M /trunk/src/callbacks.c Fix up initialisation of menu_item in on_model_toolbar_rot_trans_toolbutton_show_menu(). ------------------------------------------------------------------------ r1891 | pemsley | 2009-02-18 13:54:54 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands-gui.cc Fix up small braces issue for niggly compiler. ------------------------------------------------------------------------ r1890 | b.lohkamp | 2009-02-18 12:39:52 +0000 (Wed, 18 Feb 2009) | 1 line Changed paths: M /trunk/src/c-interface-preferences.cc user_defined_click allows only >0 no of clicks ------------------------------------------------------------------------ r1889 | kevin.cowtan | 2009-02-18 08:48:46 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc Get the normal and difference map the right way round when reading CNS files. ------------------------------------------------------------------------ r1888 | b.lohkamp | 2009-02-17 22:43:57 +0000 (Tue, 17 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/src/graphics-info.cc cleaned up and fixed python user_defined_click ------------------------------------------------------------------------ r1887 | pemsley | 2009-02-17 12:55:23 +0000 (Tue, 17 Feb 2009) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc Fix the problem of the scroll buttons all being on (use map_is_displayed() not mol_is_displayed()). ------------------------------------------------------------------------ r1886 | b.lohkamp | 2009-02-16 23:01:01 +0000 (Mon, 16 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/graphics-info.cc python: user_defined_click fixes and merge_solvent_chains funcn ------------------------------------------------------------------------ r1885 | pemsley | 2009-02-16 18:43:14 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build-gui.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/junk.cc Apply potential fix to ChainID transfer-related crash noted by Bob Nolte. ------------------------------------------------------------------------ r1884 | b.lohkamp | 2009-02-16 14:26:01 +0000 (Mon, 16 Feb 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/extensions.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/nsv.cc add 'menu button' to MFR dialog to select rotation mode: this changes the label of the button too and is synchronised with the model toobar ------------------------------------------------------------------------ r1883 | pemsley | 2009-02-16 13:39:29 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Trivial formatting changes. (elipsis) ------------------------------------------------------------------------ r1882 | pemsley | 2009-02-16 13:37:52 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.6-pre-1.xpm Update the pre-release splashscreen. ------------------------------------------------------------------------ r1881 | pemsley | 2009-02-16 12:45:34 +0000 (Mon, 16 Feb 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade A /trunk/pixmaps/coot-0.6-pre-1.xpm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c New splash screen for pre-release (long overdue). Add some interferface for renderman output (not useful currently). ------------------------------------------------------------------------ r1880 | pemsley | 2009-02-16 12:43:07 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/scheme/ncs.scm Fix up NCS jumping on heterodimers. ------------------------------------------------------------------------ r1879 | pemsley | 2009-02-16 00:40:50 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Adjust the X scale for burn-up graph. ------------------------------------------------------------------------ r1878 | pemsley | 2009-02-16 00:05:07 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/ligand/rotamer.cc Remove debugging. ------------------------------------------------------------------------ r1877 | pemsley | 2009-02-15 16:50:08 +0000 (Sun, 15 Feb 2009) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/mgtree.h M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/ligand.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/molecule-class-info-other.cc Include Stuart's new mgtree.cc, which has the forced torsions. Use atom quads in various ligand functions to support this. Adjust logic of cluser_from_point so that it works when we start from within a cluster. ------------------------------------------------------------------------ r1876 | kevin.cowtan | 2009-02-13 14:24:13 +0000 (Fri, 13 Feb 2009) | 3 lines Changed paths: M /trunk/src/callbacks.c Tidy up the console output slightly when auto-open fails. I don't really understand the fallback path here. ------------------------------------------------------------------------ r1875 | b.lohkamp | 2009-02-13 13:52:00 +0000 (Fri, 13 Feb 2009) | 1 line Changed paths: M /trunk/python-tests/03_ligand.py added python test for dictionary replace ------------------------------------------------------------------------ r1874 | pemsley | 2009-02-13 13:43:12 +0000 (Fri, 13 Feb 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/src/c-interface-validate.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Dynaramas are now labelled with the molecule name. Add ligand Search radiobuttons to gtk1 interface. ------------------------------------------------------------------------ r1873 | pemsley | 2009-02-13 00:44:01 +0000 (Fri, 13 Feb 2009) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/03-ligand.scm M /trunk/rel-todo On chem_comp, delete the previous entry with this comp_id from the restraints dictionary. Test added. ------------------------------------------------------------------------ r1872 | pemsley | 2009-02-13 00:42:10 +0000 (Fri, 13 Feb 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Documentation for overwriting restraints from a mmCIF file. ------------------------------------------------------------------------ r1871 | pemsley | 2009-02-12 14:53:52 +0000 (Thu, 12 Feb 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc Add Radio buttons for "Search here" in Ligand fitting. Remove remaining GSList scroll group code. ------------------------------------------------------------------------ r1870 | pemsley | 2009-02-12 13:58:42 +0000 (Thu, 12 Feb 2009) | 3 lines Changed paths: M /trunk/configure.in M /trunk/macros/clipper.m4 Test for clipper::CNS_HKLfile now that we depend on it. Improve message when clipper config fails. ------------------------------------------------------------------------ r1869 | pemsley | 2009-02-12 13:08:56 +0000 (Thu, 12 Feb 2009) | 2 lines Changed paths: M /trunk/configure.in A new version of clipper is required - update configure.in ------------------------------------------------------------------------ r1868 | pemsley | 2009-02-12 10:04:03 +0000 (Thu, 12 Feb 2009) | 2 lines Changed paths: M /trunk/macros/net-http-goosh.m4 M /trunk/scheme/coot-utils.scm Unfink the goosh usage. ------------------------------------------------------------------------ r1867 | pemsley | 2009-02-12 10:00:09 +0000 (Thu, 12 Feb 2009) | 5 lines Changed paths: M /trunk/libtool M /trunk/macros/net-http-goosh.m4 M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h Fix for the Display Manager scroll group. Now we don't mess with the scroll group - but instead let GTK+ manage the scroll group via widgets. GSList scroll group functions removed. get_radio_butto_in_scroll_group() added. Ligand cluster here flag enabled - no gui to activate thet setting yet. ------------------------------------------------------------------------ r1866 | pemsley | 2009-02-12 09:55:45 +0000 (Thu, 12 Feb 2009) | 2 lines Changed paths: A /trunk/src/canvas-fixes.hh M /trunk/src/nsv.cc Fix up canvas define problems. ------------------------------------------------------------------------ r1865 | kevin.cowtan | 2009-02-11 16:04:39 +0000 (Wed, 11 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Add functions to auto-open CNS-Coot interchange files (new 2009 format from AB) ------------------------------------------------------------------------ r1864 | pemsley | 2009-02-10 22:16:27 +0000 (Tue, 10 Feb 2009) | 4 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc Fix up problem of running Python code in run_user_defined_click_func, where the python function is not defined (because the scm one *is*). Now we check both scm and python against being non-default before running. ------------------------------------------------------------------------ r1863 | pemsley | 2009-02-10 19:59:34 +0000 (Tue, 10 Feb 2009) | 3 lines Changed paths: M /trunk/src/nsv.cc M /trunk/src/nsv.hh Tinker with new sequence view, now highlight in moccasin, rectangle placement adjusted. ------------------------------------------------------------------------ r1862 | pemsley | 2009-02-10 17:01:41 +0000 (Tue, 10 Feb 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Update build it scripts, using new clipper. ------------------------------------------------------------------------ r1861 | b.lohkamp | 2009-02-10 16:24:43 +0000 (Tue, 10 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py add pythonic lsq by atom test ------------------------------------------------------------------------ r1860 | pemsley | 2009-02-09 17:51:29 +0000 (Mon, 09 Feb 2009) | 3 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface.h A /trunk/src/get-residue.cc A /trunk/src/get-residue.hh M /trunk/src/nsv.cc M /trunk/src/nsv.hh Adjustments to the new sequence view, setting up to highlight the block on mouse enter. ------------------------------------------------------------------------ r1859 | pemsley | 2009-02-09 01:52:20 +0000 (Mon, 09 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface-ligands.cc Move ligand GUI functions into c-interface-ligands-gui.cc ------------------------------------------------------------------------ r1858 | pemsley | 2009-02-09 01:46:37 +0000 (Mon, 09 Feb 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1857 | pemsley | 2009-02-08 23:45:32 +0000 (Sun, 08 Feb 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/base-pairing.cc M /trunk/ligand/base-pairing.hh M /trunk/ligand/ideal-rna.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Watson Crick base pairing added. Added watson_crick_pair() to scripting layer. Added to Other Modelling Tools GUI. Test for LSQ by atom added. ------------------------------------------------------------------------ r1856 | b.lohkamp | 2009-02-08 14:36:20 +0000 (Sun, 08 Feb 2009) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h update python tests (seg id tests) add segid to python residue_info add python functions (not tested) and USE_GUILE protection: add_lsq_atom_pair, atom_spec_to_py, user_defined_click... ------------------------------------------------------------------------ r1855 | pemsley | 2009-02-07 21:04:06 +0000 (Sat, 07 Feb 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h Start work on atom-based lsq matching. update (pre) release notes (not done since release). ------------------------------------------------------------------------ r1854 | pemsley | 2009-02-07 15:05:43 +0000 (Sat, 07 Feb 2009) | 6 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coot-utils/coot-coord-extras.cc M /trunk/greg-tests/begin.grg M /trunk/happy-coot-diary.html M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/nsv.cc Add debugging to Bond_lines.cc, trying to find this stared atom bonding problem. Not fixed yet. get-atom added to coot-utils.scm (from testing begin.grg). Add user-defined-click function. Given params: n-clicks func. New sequence view put in place. ------------------------------------------------------------------------ r1853 | pemsley | 2009-02-06 16:55:38 +0000 (Fri, 06 Feb 2009) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc Test for RNA base mutation name - canonical base name function added. Test for SegIDs on mutation, NCS copy and add terminal residue. A residue-info returns info about segid too now. mutate_base() exposed to scripting layer. ------------------------------------------------------------------------ r1852 | b.lohkamp | 2009-02-06 09:34:37 +0000 (Fri, 06 Feb 2009) | 1 line Changed paths: M /trunk/src/post-process-coot-wrap-guile.sh fix for post processing wrap guile in windows ------------------------------------------------------------------------ r1851 | pemsley | 2009-02-06 08:55:08 +0000 (Fri, 06 Feb 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Fix up rot/trans mode so that residue zone works again. ------------------------------------------------------------------------ r1850 | pemsley | 2009-02-06 07:23:25 +0000 (Fri, 06 Feb 2009) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc Use old-style function to get the group from the scroll radio button. Comment out the debugging printfs for the scroll group. ------------------------------------------------------------------------ r1849 | pemsley | 2009-02-06 01:05:13 +0000 (Fri, 06 Feb 2009) | 3 lines Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h Apply a fix (hopefully) for the display manager delete molecule bug. save the (new) radio button group by using a "group-changed" callback. ------------------------------------------------------------------------ r1848 | pemsley | 2009-02-05 23:47:36 +0000 (Thu, 05 Feb 2009) | 10 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/Makefile.am D /trunk/ligand/atom-quads.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/mini-mol/Makefile.am A /trunk/mini-mol/atom-quads.hh (from /trunk/ligand/atom-quads.hh:1834) M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Add get_torsion() method to minimols' residue - for testing ligand dihedrals. Move atom-quads.hh to minimol to asist. Add torsioned_atoms_info_t to wligand.hh for testing dihedrals. get_gslist_for_scroll_in_display_manager() method added in attempt to fix display manager delete map bug. (no fix) test_internal_single() exposed to the scripting layer. get_geometry_torsion() split out from display_geometry_torsion(). Don't try to use the GUI when no ligands found in --no-graphics mode. get_atom() from atom spec method added to molecule_class_info_t. ------------------------------------------------------------------------ r1847 | pemsley | 2009-02-05 19:50:20 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Extend x axis to 60 days. ------------------------------------------------------------------------ r1846 | pemsley | 2009-02-05 19:17:13 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1845 | pemsley | 2009-02-05 18:31:43 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/command-line.cc Add in extra flags for --help. ------------------------------------------------------------------------ r1844 | pemsley | 2009-02-05 18:30:48 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/main.cc Add a note about gtk version. ------------------------------------------------------------------------ r1843 | pemsley | 2009-02-05 18:28:22 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r1842 | pemsley | 2009-02-05 18:27:20 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1841 | pemsley | 2009-02-05 18:26:08 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh map_fill_from_mtz now returns a bool (about the state of the map). ------------------------------------------------------------------------ r1840 | pemsley | 2009-02-05 18:25:12 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add an output operator for dict_torsion_restraint_t. ------------------------------------------------------------------------ r1839 | pemsley | 2009-02-05 18:24:24 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Add some extra text, suggesting making core dump. ------------------------------------------------------------------------ r1838 | pemsley | 2009-02-05 01:46:31 +0000 (Thu, 05 Feb 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Rot/Trans: Set the mmdb_manager properly in the case of ROT_TRANS_TYPE_ZONE. Fixes crash. ------------------------------------------------------------------------ r1837 | pemsley | 2009-02-05 01:30:11 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/fixup-gtk2-interface.sh A /trunk/src/gtk2-interface-rot-trans-fixup.awk M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh More post-processing of the gtk2 interface file, for old GTKs. ------------------------------------------------------------------------ r1836 | pemsley | 2009-02-05 00:40:42 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c Fixup: use #ifdef GTK_TYPE_MENU_TOOL_BUTTON ------------------------------------------------------------------------ r1835 | pemsley | 2009-02-05 00:04:22 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/callbacks.h More protection of menu tool buttons for old gtks. ------------------------------------------------------------------------ r1834 | b.lohkamp | 2009-02-04 14:09:41 +0000 (Wed, 04 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/libcheck.py fixed libcheck.py, returns imol now ------------------------------------------------------------------------ r1833 | pemsley | 2009-02-04 13:42:50 +0000 (Wed, 04 Feb 2009) | 6 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.h M /trunk/src/coot.i M /trunk/src/coot_pythonmodule.cc M /trunk/src/coot_wrap_guile.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/main.cc M /trunk/src/post-process-coot-wrap-guile.sh Try again using NEW_COORDS_ADD. Fix problem of rotation atom missing (hence crash) when rotating whole molecule, needed a util function to transfer a whole molecule (with atom index transfer) because the chain-ids of residue selection were mis-applied. Add some includes of cstdios for gmp.h from libguile.h. ------------------------------------------------------------------------ r1832 | pemsley | 2009-02-04 13:32:20 +0000 (Wed, 04 Feb 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add fnction to create an mmdb manager from mmdb manager, with atom index transfer. ------------------------------------------------------------------------ r1831 | pemsley | 2009-02-04 09:22:20 +0000 (Wed, 04 Feb 2009) | 2 lines Changed paths: M /trunk/src/main.cc RHEL 4 (Gtk 2.4.13) does not have gtk_menu_tool_buttons. ------------------------------------------------------------------------ r1830 | b.lohkamp | 2009-02-03 18:57:43 +0000 (Tue, 03 Feb 2009) | 1 line Changed paths: M /trunk/python/coot_gui.py clean up fill_option_menu functions in coot_gui.py ------------------------------------------------------------------------ r1829 | b.lohkamp | 2009-02-03 16:54:44 +0000 (Tue, 03 Feb 2009) | 3 lines Changed paths: M /trunk/ligand/richardson-rotamers.cc M /trunk/src/main.cc fix proline rotamers radio check menus for rotate translate ------------------------------------------------------------------------ r1828 | b.lohkamp | 2009-02-03 14:45:08 +0000 (Tue, 03 Feb 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/libcheck.py M /trunk/python-tests/03_ligand.py M /trunk/scheme/extensions.scm M /trunk/src/callbacks.c M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h update libcheck python scripting pythonic replace residue (mutate-by-overlap) fix preferences (and gtk warnings) for new rot-trans toolbutton add -oldpdb to reduce command ------------------------------------------------------------------------ r1827 | pemsley | 2009-02-03 14:20:00 +0000 (Tue, 03 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm Fix up typo in dipole test as per Bernhard's suggestion. ------------------------------------------------------------------------ r1826 | pemsley | 2009-02-03 12:10:37 +0000 (Tue, 03 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/begin.grg remove (turn-on-debugging) - tests fail. ------------------------------------------------------------------------ r1825 | b.lohkamp | 2009-02-03 08:19:50 +0000 (Tue, 03 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/03_ligand.py update python tests ------------------------------------------------------------------------ r1824 | pemsley | 2009-02-02 23:27:23 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/mini-mol/mini-mol.cc Include algorithm, needed for std::sort(). ------------------------------------------------------------------------ r1823 | pemsley | 2009-02-02 23:08:57 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c Don't run GtkMenuToolButton for gtk1. ------------------------------------------------------------------------ r1822 | pemsley | 2009-02-02 21:31:24 +0000 (Mon, 02 Feb 2009) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/src/globjects.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc update_map_in_display_control_widget() was being called in initialize_map_things_on_read_molecule(). But we can't do that until xmap_is_filled[0] is set. So move update_map_in_display_control_widget() into the calling function after xmap_is_filled[0] is set. ------------------------------------------------------------------------ r1821 | pemsley | 2009-02-02 19:21:29 +0000 (Mon, 02 Feb 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc Add rotate translate mode change to the GUI with a menutoolbar. It gets set up in main.cc ------------------------------------------------------------------------ r1820 | pemsley | 2009-02-02 15:16:10 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/rel-todo M /trunk/scheme/generic-objects.scm Add -oldpdb to the arguments to reduce. ------------------------------------------------------------------------ r1819 | pemsley | 2009-02-02 14:11:58 +0000 (Mon, 02 Feb 2009) | 3 lines Changed paths: M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/residue_by_phi_psi.cc M /trunk/ligand/residue_by_phi_psi.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info.cc Fix the B-factor test of add-terminal-residue test failure by passing the b-factor to residue_by_phi_psi constructor. ------------------------------------------------------------------------ r1818 | pemsley | 2009-02-02 01:05:11 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm In addition to previous, sort-chains uses a minimol function and a test is added. ------------------------------------------------------------------------ r1817 | pemsley | 2009-02-02 01:04:27 +0000 (Mon, 02 Feb 2009) | 5 lines Changed paths: M /trunk/coords/mmdb-crystal.cc M /trunk/db-main/db-main.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/high-res/coot-atom-graph.cc M /trunk/high-res/high-res.cc M /trunk/ideal/regularize-minimol.cc M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/helix-placement.cc M /trunk/ligand/residue_by_phi_psi.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/mini-mol/testminimol.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Add a b-factor to a minimol atom. Lots of small changes in the use of the constructors then. pcmmdbmanager() no longer takes a bfactor arg, as the atoms have b-factors now. ------------------------------------------------------------------------ r1816 | pemsley | 2009-02-01 17:23:47 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1815 | pemsley | 2009-02-01 17:23:05 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm M /trunk/ligand/dipole.cc M /trunk/rel-todo Add dipole test (and fix up code). ------------------------------------------------------------------------ r1814 | pemsley | 2009-02-01 17:19:33 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Fix syntax error. ------------------------------------------------------------------------ r1813 | pemsley | 2009-02-01 15:58:16 +0000 (Sun, 01 Feb 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/scheme/libcheck.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add function assign_hetatms() and use it after reading a file from libcheck. Introduce function PDB_standard_residue_types() - used in conditionally assigning HETATMs. ------------------------------------------------------------------------ r1812 | pemsley | 2009-02-01 15:46:13 +0000 (Sun, 01 Feb 2009) | 10 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/happy-coot-diary.html M /trunk/scheme/coot-gui.scm M /trunk/scheme/libcheck.scm M /trunk/src/Makefile.am A /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c A /trunk/src/guile-fixups.h Better handle the case where libcheck is not found. monomer-molecule-from-3-let-code reworked. Now we check for libcheck in the path and split out the reading of the cif and pdb files from the running of libcheck (those files could already exist and therefore we can just read them even if libcheck is not in path). Also a warning text in the monomer dialog is shown if libcheck is not found (the is tested with a scripting function (not yet implemented for the python path). src/c-interface-ligands-gui.cc added. ------------------------------------------------------------------------ r1811 | pemsley | 2009-02-01 13:50:45 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-waters.cc M /trunk/src/gtk2-interface.c Add protein->water distance cut offs to the GUI. ------------------------------------------------------------------------ r1810 | pemsley | 2009-01-31 17:27:35 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/rel-todo update todo list and add a picure to diary. ------------------------------------------------------------------------ r1809 | pemsley | 2009-01-31 14:00:23 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm Add a GUI for mutate-by-overlap (Replace residue). Needs a python version. ------------------------------------------------------------------------ r1808 | pemsley | 2009-01-31 09:25:18 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary, fix syntax error. ------------------------------------------------------------------------ r1807 | pemsley | 2009-01-31 08:00:12 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1806 | pemsley | 2009-01-30 17:27:08 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix the RHEL 4 64-bit python build tag. ------------------------------------------------------------------------ r1805 | pemsley | 2009-01-30 16:17:52 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm RHEL 4, 64-bit python-enabled builds. ------------------------------------------------------------------------ r1804 | pemsley | 2009-01-30 09:33:44 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1803 | pemsley | 2009-01-30 09:33:29 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py tinker with burn up graph. ------------------------------------------------------------------------ r1802 | pemsley | 2009-01-30 09:32:03 +0000 (Fri, 30 Jan 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/molecule-class-info.cc Add a function to mark atoms as HETATMs and use it in the addition of pointer atoms. ------------------------------------------------------------------------ r1801 | pemsley | 2009-01-30 00:16:09 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo Another item on the TODO list. ------------------------------------------------------------------------ r1800 | pemsley | 2009-01-29 20:36:51 +0000 (Thu, 29 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Add binaries for RHEL 4 64-bit in Oxford. ------------------------------------------------------------------------ r1799 | pemsley | 2009-01-29 00:35:44 +0000 (Thu, 29 Jan 2009) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc small tidy up of formatting. ------------------------------------------------------------------------ r1798 | b.lohkamp | 2009-01-27 20:01:22 +0000 (Tue, 27 Jan 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/gap.py M /trunk/scheme/gap.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc fit-gap: fix python version and make guile to accept assigned sequence various fixes for python functions esp. add_dipole i.e. returns the right result now ------------------------------------------------------------------------ r1797 | pemsley | 2009-01-27 12:14:38 +0000 (Tue, 27 Jan 2009) | 4 lines Changed paths: M /trunk/ligand/dipole.cc A /trunk/pixmaps/coot-favicon.png M /trunk/src/c-interface-ligands.cc Fix up python problem - so that it compiles at least, python code does not give correct result yet for add_dipole(). ------------------------------------------------------------------------ r1796 | pemsley | 2009-01-27 09:30:54 +0000 (Tue, 27 Jan 2009) | 5 lines Changed paths: M /trunk/README M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/shelx-extensions.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add_dipole functions should return a dipole. SCM version filled. Fails (non-committed) test currently. Add editable shelxl text gui. Pass fixed atom specs in refine from residues vec. ------------------------------------------------------------------------ r1795 | pemsley | 2009-01-27 06:33:00 +0000 (Tue, 27 Jan 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-modelling.cc In generate_molecule_and_refine() add in settings for sec struct and rama restraints. ------------------------------------------------------------------------ r1794 | pemsley | 2009-01-27 05:11:09 +0000 (Tue, 27 Jan 2009) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Tweak tutorial name. ------------------------------------------------------------------------ r1793 | pemsley | 2009-01-26 14:11:08 +0000 (Mon, 26 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New axes for burn-up graph. ------------------------------------------------------------------------ r1792 | b.lohkamp | 2009-01-20 21:18:46 +0000 (Tue, 20 Jan 2009) | 1 line Changed paths: M /trunk/python/gap.py fit_gap (python) accepts assigned sequence ------------------------------------------------------------------------ r1791 | b.lohkamp | 2009-01-20 15:50:19 +0000 (Tue, 20 Jan 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c update refmac gui (TLS and SAD) to look like new CCP4i GUI side-by-side stereo with anti-aliasing and background colour change ------------------------------------------------------------------------ r1790 | pemsley | 2009-01-20 14:07:44 +0000 (Tue, 20 Jan 2009) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Update ubuntu builds to 8.04.2 ------------------------------------------------------------------------ r1789 | b.lohkamp | 2009-01-20 08:21:00 +0000 (Tue, 20 Jan 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/macros/Makefile.am M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h added add_dipole_for_residue in python add lib-prefix.m4 to dist fix set position of 'Go to Atom' dialog refine_residues_py returns True when map found and refinement was executed ------------------------------------------------------------------------ r1788 | pemsley | 2009-01-19 00:16:54 +0000 (Mon, 19 Jan 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc Add a method to turn off shadows in the file created for raster3d's render. ------------------------------------------------------------------------ r1787 | pemsley | 2009-01-17 16:18:57 +0000 (Sat, 17 Jan 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/ligand/dipole.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.cc Add some protection and info for dipole construction failure. More protection in residues_near_residue(). ------------------------------------------------------------------------ r1786 | pemsley | 2009-01-17 15:20:34 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Yet more protection in residues_near_residue(). ------------------------------------------------------------------------ r1785 | pemsley | 2009-01-17 15:19:52 +0000 (Sat, 17 Jan 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Make sure that n_res_atoms is sane before proceeding with residues_near_residue(). ------------------------------------------------------------------------ r1784 | pemsley | 2009-01-17 15:10:41 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc #define guile functions for backward compatibility. ------------------------------------------------------------------------ r1783 | pemsley | 2009-01-17 14:17:32 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add interface to add dipole from multiple residues - e.g. an active site. ------------------------------------------------------------------------ r1782 | pemsley | 2009-01-17 12:57:50 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h add_dipole() should return the dipole number. ------------------------------------------------------------------------ r1781 | pemsley | 2009-01-17 02:06:27 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1780 | pemsley | 2009-01-16 21:08:52 +0000 (Fri, 16 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo Add a few more problems to rel-todo. ------------------------------------------------------------------------ r1779 | b.lohkamp | 2009-01-16 16:11:30 +0000 (Fri, 16 Jan 2009) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/pixmaps/torsion-general.svg M /trunk/python-tests/01_pdb_mtz.py fix font for torsion-general.svg update python add terminal residue test (b-factors) ------------------------------------------------------------------------ r1778 | pemsley | 2009-01-16 13:31:53 +0000 (Fri, 16 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-mutate.cc Remove debugging. ------------------------------------------------------------------------ r1777 | pemsley | 2009-01-16 13:31:35 +0000 (Fri, 16 Jan 2009) | 5 lines Changed paths: M /trunk/burn-up/new-graph.py M /trunk/coot-utils/coot-coord-utils.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/mini-mol/mini-mol.cc M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc Apply default B factor in minimol's pcmmdbmanager(). Apply default B factor in add_side_chain_to_terminal_res(). Add a test for B factors in add terminal residue. Burn up graph extended to 40 days. ------------------------------------------------------------------------ r1776 | b.lohkamp | 2009-01-14 16:58:02 +0000 (Wed, 14 Jan 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.h make_residue_spec and refine_residues for python ------------------------------------------------------------------------ r1775 | pemsley | 2009-01-14 13:49:33 +0000 (Wed, 14 Jan 2009) | 8 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/burn-up/new-graph.py M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc In generate_molecule_and_refine use have_dictionary_for_residue_types() to try to load all the dictionary restraints before making restraints. init_refmac_mon_lib() now returns non-zero when cif contains only links. residue_types_in_residue_vec() utility function added. Tinker with web page builder. Testing to get the python logs correctly linked. ------------------------------------------------------------------------ r1774 | pemsley | 2009-01-13 18:12:07 +0000 (Tue, 13 Jan 2009) | 7 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/doc/user-manual.texi M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXCreator.h M /trunk/surface/Makefile.am Add dipole function, fill_charged_atoms, used in apply_charges in the molecule class. apply_charges sets charges to CXX_UNSET_CHARGE, which gets tested for in CXXCreator. make_surface() now takes a protein_geometry argument. Trap a null chain in sequence-view.cc ------------------------------------------------------------------------ r1773 | b.lohkamp | 2009-01-13 17:53:24 +0000 (Tue, 13 Jan 2009) | 1 line Changed paths: A /trunk/macros/lib-prefix.m4 add lib-prefix.m4 macro to use $acl_libdirstem ------------------------------------------------------------------------ r1772 | b.lohkamp | 2009-01-13 16:37:57 +0000 (Tue, 13 Jan 2009) | 3 lines Changed paths: M /trunk/bldnotes A /trunk/bldnotes-2008 M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c split and update (bl)dnotes combobox for recentre options in coordinates filechooser ------------------------------------------------------------------------ r1771 | b.lohkamp | 2009-01-13 13:19:03 +0000 (Tue, 13 Jan 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/graphics-info.cc updated python tests python functions: residues_near_position_py, run_post_manipulation_hook_py, non_standard_residue_names_py fix python functions: map_peaks_py and map_peaks_near_point_py ------------------------------------------------------------------------ r1770 | pemsley | 2009-01-12 21:01:06 +0000 (Mon, 12 Jan 2009) | 7 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Residue type CL support in refinement. Geometry function added have_dictionary_for_residue_types(). Cif dictionary read success now based on the number of atoms read, not the number of bonds. Switch to rigid body refine uses check_for_no_restraints_object(), not just for waters. ------------------------------------------------------------------------ r1769 | pemsley | 2009-01-12 19:02:03 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Tinker with the ticks. ------------------------------------------------------------------------ r1768 | pemsley | 2009-01-12 17:48:36 +0000 (Mon, 12 Jan 2009) | 5 lines Changed paths: M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc write_residue_range_to_pdb_file() returns the correct error code and now writes out the the same chain-id as is input. Refactor (almost) duplicated update_refinement_atoms() code. Remove some debugging from residue vector refinement code. ------------------------------------------------------------------------ r1767 | pemsley | 2009-01-12 16:34:34 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/Makefile.am A /trunk/src/graphics-info-gui.cc A /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.cc split graphics-info.cc into better sized chunks, splitting out the refmac functions. ------------------------------------------------------------------------ r1766 | pemsley | 2009-01-12 16:07:02 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/c-interface-preferences.cc M /trunk/src/gtk2-interface.c Fix up generic_object_clear(). ------------------------------------------------------------------------ r1765 | pemsley | 2009-01-12 16:05:11 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix up missing menu items. ------------------------------------------------------------------------ r1764 | pemsley | 2009-01-12 14:29:39 +0000 (Mon, 12 Jan 2009) | 3 lines Changed paths: M /trunk/ligand/find-waters.cc M /trunk/rel-todo M /trunk/src/graphics-info.cc Fix findwaters for use with a map. Fix strange rezooming behaviour of reset view. ------------------------------------------------------------------------ r1763 | pemsley | 2009-01-12 14:12:39 +0000 (Mon, 12 Jan 2009) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc Fix up the problem of bonding across gaps in geometry validation (and elsewhere, presumably). ------------------------------------------------------------------------ r1762 | pemsley | 2009-01-12 11:47:23 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update the clipper version in gtk build script. ------------------------------------------------------------------------ r1761 | pemsley | 2009-01-12 11:46:22 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/dnotes Fix the prefix use in the version of clipper. ------------------------------------------------------------------------ r1760 | pemsley | 2009-01-11 21:29:25 +0000 (Sun, 11 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1759 | pemsley | 2009-01-11 10:56:56 +0000 (Sun, 11 Jan 2009) | 2 lines Changed paths: M /trunk/build-it Fix the incorrect use of latest in clipper tar file. ------------------------------------------------------------------------ r1758 | pemsley | 2009-01-10 12:24:29 +0000 (Sat, 10 Jan 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc Check for out of ordered residues when no restraints found and add extra info to the dialog in that case. ------------------------------------------------------------------------ r1757 | pemsley | 2009-01-10 11:37:04 +0000 (Sat, 10 Jan 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/molecule-class-info.cc Scale the dipoles. reorder rel-todo. ------------------------------------------------------------------------ r1756 | pemsley | 2009-01-10 11:11:59 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: A /trunk/dnotes M /trunk/rel-todo dnotes added - now with all Release, Fixed and Done items removed. ------------------------------------------------------------------------ r1755 | pemsley | 2009-01-10 10:58:20 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: D /trunk/dnote-2008 A /trunk/dnotes-2008 (from /trunk/dnote-2008:1754) The end of 2008 is when these notes stopped being updated. New notes introduced. ------------------------------------------------------------------------ r1754 | pemsley | 2009-01-10 10:57:16 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: A /trunk/dnote-2008 (from /trunk/dnotes:1751) D /trunk/dnotes Move dnotes. ------------------------------------------------------------------------ r1753 | pemsley | 2009-01-10 10:51:10 +0000 (Sat, 10 Jan 2009) | 4 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/rel-todo M /trunk/src/nsv.cc More update on the sequence viewer, not it seems the right size and does action on click. Reorder the binary builds page. ------------------------------------------------------------------------ r1752 | pemsley | 2009-01-10 10:49:44 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix the python variable for the installed config file. ------------------------------------------------------------------------ r1751 | pemsley | 2009-01-09 18:31:27 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/scheme/libcheck.scm M /trunk/src/nsv.cc M /trunk/src/nsv.hh More playing with nsv canvas parameter - not right yet. ------------------------------------------------------------------------ r1750 | pemsley | 2009-01-09 18:30:08 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Use scm_is_true() not gh_scm2bool() in get_monomer(). ------------------------------------------------------------------------ r1749 | pemsley | 2009-01-09 16:54:37 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm No more FC6 for setsuko, now we have fedora-8 and fedora-10. ------------------------------------------------------------------------ r1748 | pemsley | 2009-01-09 14:52:41 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix up optim/debugging option for compiling on x84_64 (well, Centos5 at least). ------------------------------------------------------------------------ r1747 | pemsley | 2009-01-09 14:51:18 +0000 (Fri, 09 Jan 2009) | 3 lines Changed paths: M /trunk/src/nsv.cc M /trunk/src/nsv.hh Enable go to atom on letter click - using intelligent_this_residue_mmdb_atom(). ------------------------------------------------------------------------ r1746 | pemsley | 2009-01-09 13:33:02 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Update burn-up files to reference. ------------------------------------------------------------------------ r1745 | pemsley | 2009-01-09 08:59:49 +0000 (Fri, 09 Jan 2009) | 3 lines Changed paths: M /trunk/build-it M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/rel-todo M /trunk/src/geometry-graphs.cc M /trunk/src/nsv.cc M /trunk/src/nsv.hh Updates to nsv. Now we can click on a residues letter, but go to atom/residue not enabled yet. ------------------------------------------------------------------------ r1744 | pemsley | 2009-01-08 21:07:04 +0000 (Thu, 08 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/generic-display-object.hh Add clear method for generic object - needs a test. ------------------------------------------------------------------------ r1743 | pemsley | 2009-01-08 12:24:50 +0000 (Thu, 08 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/globjects.cc Fix problem filling map peak points vector. ------------------------------------------------------------------------ r1742 | pemsley | 2009-01-08 01:52:54 +0000 (Thu, 08 Jan 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc map-peaks near point function added. In scm and python.o Util function create_mmdbmanager_from_atom() created. peak-search's make_sample_protein_coords() can now take a every_nth arg. ------------------------------------------------------------------------ r1741 | pemsley | 2009-01-07 16:23:58 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/burn-up/new-graph.py M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h Add map_peaks functions, Python version is filled, scm version is not. ------------------------------------------------------------------------ r1740 | b.lohkamp | 2009-01-07 13:06:10 +0000 (Wed, 07 Jan 2009) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fix python sphere selection test ------------------------------------------------------------------------ r1739 | b.lohkamp | 2009-01-07 12:09:25 +0000 (Wed, 07 Jan 2009) | 1 line Changed paths: M /trunk/src/testing.cc windows jiggery fix for testing.cc ------------------------------------------------------------------------ r1738 | b.lohkamp | 2009-01-07 09:02:44 +0000 (Wed, 07 Jan 2009) | 1 line Changed paths: M /trunk/python/generic_objects.py M /trunk/src/molecule-class-info-ribbons.cc fix generic objects gui python bug ------------------------------------------------------------------------ r1737 | pemsley | 2009-01-07 06:19:48 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/ligand/Makefile.am No libccp4mg-pygl_coord.la dependency for findwaters_real. ------------------------------------------------------------------------ r1736 | pemsley | 2009-01-07 00:23:09 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc guile tweaks for 1.6 usage. ------------------------------------------------------------------------ r1735 | pemsley | 2009-01-07 00:13:43 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/src/nsv.cc gtk_canvas_new not gnome_canvas_new (not yet, anyway). ------------------------------------------------------------------------ r1734 | pemsley | 2009-01-07 00:03:18 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/autogen.sh M /trunk/src/molecule-class-info-residues.cc M /trunk/src/nsv.cc More tweaks to make a build on gtk1 system. Now we use gettext macros. ------------------------------------------------------------------------ r1733 | pemsley | 2009-01-06 23:59:39 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Fix up python macro that uses $acl_libdirstem. ------------------------------------------------------------------------ r1732 | pemsley | 2009-01-06 23:18:10 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/gtk-manual.cc make GDK_WINDOW_TYPE_HINT_SPLASHSCREEN GTK2 specific. ------------------------------------------------------------------------ r1731 | pemsley | 2009-01-06 23:16:25 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Fix up the python hook function name. ------------------------------------------------------------------------ r1730 | pemsley | 2009-01-06 21:50:55 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Add fixups for old versions of guile. ------------------------------------------------------------------------ r1729 | pemsley | 2009-01-06 21:04:30 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix return typ for python function. ------------------------------------------------------------------------ r1728 | pemsley | 2009-01-06 20:39:58 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: A /trunk/src/nsv.cc A /trunk/src/nsv.hh Add forgotten nsv files. ------------------------------------------------------------------------ r1727 | pemsley | 2009-01-06 19:18:26 +0000 (Tue, 06 Jan 2009) | 42 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb.cc M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/test-utils.cc M /trunk/density-contour/CIsoSurface.cpp M /trunk/dnotes M /trunk/doc/coot-shelx.tex M /trunk/doc/crib-sheet.tex M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/high-res/Makefile.am M /trunk/ideal/test-indexing.cc M /trunk/ligand/Makefile.am A /trunk/ligand/base-pairing.cc A /trunk/ligand/base-pairing.hh A /trunk/ligand/dipole.cc A /trunk/ligand/dipole.hh M /trunk/ligand/ideal-rna.cc M /trunk/ligand/ideal-rna.hh M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/macros/mmdb-ssm.m4 M /trunk/macros/mmdb.m4 M /trunk/macros/with-python.m4 M /trunk/mapview.glade M /trunk/rel-todo M /trunk/scheme/coot-crash-catcher.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/generic-objects.scm M /trunk/scheme/shelx-extensions.scm M /trunk/scheme/shelx.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am A /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot.i M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/main.cc A /trunk/src/manipulation-modes.hh M /trunk/src/mol-hierachy.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc A /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-ribbons.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh A /trunk/src/rotate-translate-modes.hh M /trunk/src/support.c M /trunk/src/testing.cc M /trunk/src/testing.hh Cuba updates: with-no-backups macro fixed. residues-need-position function added (python version needs to be filled) shelx-refine-gui added (Tobias Beck). shelx-extensions use the shelx refine gui. shelx tutorial reworked. Added test for rotamer names and probabilities. Dynamic distances mode uses pick_cursor_maybe(). probe-local-sphere added which uses write-pdb-file-for-molprobity which appends the CON files (not sure that they are needed now, with new probe). molecule-class-info-residues.cc file added. rotamer_score() function filled. Changes for segids, add function last_residue_in_chain returning a pointer to a CResidue. Util functions residue_atoms_segid() and chain_atoms_segid() used to find the segid of a residue before mutation, so that the new residue atoms have the same segid as the old atoms of the mutated residue. Util function copy_segid from residue to residue, used in insert_coords_internal() and copy_residue_range() for similar reasons. set_atom_string_attribute() extended to take a segid attribute. Dipole class and files added (in ligand dir). Functions to add, delete and render dipoles added (currently a problem with the orientation of the arrow object). create_splash_screen_window_for_file() added to work with --splash-screen command line option. Needed enhancements to support.c. cluster_from_point() added to ligand class. Tested in testing.cc, however, it uses hopelessly broken torsion setting code for wiggly ligands. Needs fixing soon - probably a re-write of the atom-tree code. start coding a new sequence view code (exptl::nsv). configure.in and macros now use $acl_libdirstem (and AC_LIB_PREPARE_MULTILIB which sets it up) - after conversation with Tim Fenn. AC_LIB_PREPARE_MULTILIB is defined in lib-prefix.m4 on the system, so that may introduce a gettext dependency for the build system. Keybinding handling changed. Now we are conservative about setting the handled flag, so that more key presses (e.g. A and S) fall through to the scripting layer. post-manipulation-hook, a variable that is check for begin a procedure, and if so, runs it after accepting moving atoms, delete or mutate. Python version needs to be filled [JED]. Added function to set the number of differences shown on the Kleywegt Plot [Clemens]. ------------------------------------------------------------------------ r1726 | pemsley | 2009-01-06 15:05:55 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: A /trunk/ccp4mg-utils/matrix.cc A /trunk/ccp4mg-utils/matrix.h Add ccp4 matrix files - they had been removed from repo. ------------------------------------------------------------------------ r1725 | pemsley | 2009-01-06 14:44:33 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/atom-utils/Makefile.am M /trunk/ccp4mg-utils/Makefile.am M /trunk/configure.in M /trunk/coords/Bond_lines.h M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/high-res/Makefile.am M /trunk/libtool M /trunk/ligand/Makefile.am M /trunk/pixmaps/torsion-general.svg M /trunk/python/coot_utils.py M /trunk/sequence-view/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot.py M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.h Revert to 1716 for main trunk. ------------------------------------------------------------------------ r1724 | pemsley | 2009-01-06 14:02:54 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.h trivial diff, the header. ------------------------------------------------------------------------ r1722 | pemsley | 2009-01-06 09:35:05 +0000 (Tue, 06 Jan 2009) | 6 lines Changed paths: M /trunk/ccp4mg-utils/mmut/mman_base.cc M /trunk/ccp4mg-utils/mmut/mman_manager.cc M /trunk/ccp4mg-utils/mmut/mman_manager.h M /trunk/ccp4mg-utils/mmut/mmut_bonds.cc M /trunk/ccp4mg-utils/mmut/mmut_colour.cc M /trunk/ccp4mg-utils/mmut/mmut_colour.h M /trunk/ccp4mg-utils/mmut/mmut_connectivity.cc M /trunk/ccp4mg-utils/mmut/mmut_hbond.cc M /trunk/ccp4mg-utils/mmut/mmut_manager.cc M /trunk/ccp4mg-utils/mmut/mmut_manager.h M /trunk/ccp4mg-utils/mmut/mmut_sasarea.cc M /trunk/ccp4mg-utils/mmut/mmut_sbase.cc M /trunk/ccp4mg-utils/mmut/mmut_sbase.h M /trunk/ccp4mg-utils/pygl/cprimitive.h M /trunk/ccp4mg-utils/util/mgtree.cc M /trunk/ccp4mg-utils/util/redirect.cc Get ccp4mg-utils to compile on GCC 4.3.2 - contains some pretty horrific kludges. It should be fixed by someone who knows the code and uses mmdb-1.19. SBASE code should be careful about const char *s. There is a bug - possibly in ccp4mg-atom_util - which causes a crash on closing Coot. ------------------------------------------------------------------------ r1721 | b.lohkamp | 2008-12-28 15:23:23 +0000 (Sun, 28 Dec 2008) | 5 lines Changed paths: M /trunk/ccp4mg-utils/pygl/texture.cc M /trunk/ligand/Makefile.am M /trunk/pixmaps/torsion-general.svg font fix for torsion-general.svg more ccp4mg include fixes remove all fancy textures in ccp4mg/pygl/textures.cc until we properly test for the GL_VERSION (this should compile on all OS) ------------------------------------------------------------------------ r1720 | b.lohkamp | 2008-12-27 23:01:04 +0000 (Sat, 27 Dec 2008) | 1 line Changed paths: M /trunk/ccp4mg-utils/pygl/texture.cc fix opengl ccp4mg texture problem on FC4 (quick fix for now) ------------------------------------------------------------------------ r1719 | b.lohkamp | 2008-12-27 18:05:33 +0000 (Sat, 27 Dec 2008) | 1 line Changed paths: M /trunk/ccp4mg-utils/Makefile.am D /trunk/ccp4mg-utils/matrix.cc D /trunk/ccp4mg-utils/matrix.h M /trunk/high-res/Makefile.am M /trunk/ligand/Makefile.am M /trunk/src/Makefile.am fix ccp4mg matrix doublication (hopefully) ------------------------------------------------------------------------ r1718 | b.lohkamp | 2008-12-27 17:04:01 +0000 (Sat, 27 Dec 2008) | 1 line Changed paths: A /trunk/src/molecule-class-info-ribbons.cc add molecule-class-info-ribbons.cc ------------------------------------------------------------------------ r1717 | b.lohkamp | 2008-12-27 16:27:53 +0000 (Sat, 27 Dec 2008) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/atom-utils/Makefile.am M /trunk/bldnotes M /trunk/ccp4mg-utils/Makefile.am A /trunk/ccp4mg-utils/get-all-new-utils.sh A /trunk/ccp4mg-utils/mmut A /trunk/ccp4mg-utils/mmut/Makefile.am A /trunk/ccp4mg-utils/mmut/mman_base.cc A /trunk/ccp4mg-utils/mmut/mman_base.h A /trunk/ccp4mg-utils/mmut/mman_manager.cc A /trunk/ccp4mg-utils/mmut/mman_manager.h A /trunk/ccp4mg-utils/mmut/mmut_basepairs.cc A /trunk/ccp4mg-utils/mmut/mmut_basepairs.h A /trunk/ccp4mg-utils/mmut/mmut_bonds.cc A /trunk/ccp4mg-utils/mmut/mmut_bonds.h A /trunk/ccp4mg-utils/mmut/mmut_colour.cc A /trunk/ccp4mg-utils/mmut/mmut_colour.h A /trunk/ccp4mg-utils/mmut/mmut_connectivity.cc A /trunk/ccp4mg-utils/mmut/mmut_connectivity.h A /trunk/ccp4mg-utils/mmut/mmut_contact.cc A /trunk/ccp4mg-utils/mmut/mmut_contact.h A /trunk/ccp4mg-utils/mmut/mmut_hbond.cc A /trunk/ccp4mg-utils/mmut/mmut_hbond.h A /trunk/ccp4mg-utils/mmut/mmut_lipids.cc A /trunk/ccp4mg-utils/mmut/mmut_lipids.h A /trunk/ccp4mg-utils/mmut/mmut_manager.cc A /trunk/ccp4mg-utils/mmut/mmut_manager.h A /trunk/ccp4mg-utils/mmut/mmut_morph.cc A /trunk/ccp4mg-utils/mmut/mmut_morph.h A /trunk/ccp4mg-utils/mmut/mmut_nma.cc A /trunk/ccp4mg-utils/mmut/mmut_nma.h A /trunk/ccp4mg-utils/mmut/mmut_sasarea.cc A /trunk/ccp4mg-utils/mmut/mmut_sasarea.h A /trunk/ccp4mg-utils/mmut/mmut_sbase.cc A /trunk/ccp4mg-utils/mmut/mmut_sbase.h A /trunk/ccp4mg-utils/mmut/mmut_secstr.cc A /trunk/ccp4mg-utils/mmut/mmut_secstr.h A /trunk/ccp4mg-utils/mmut/mmut_spline.cc A /trunk/ccp4mg-utils/mmut/mmut_util.cc A /trunk/ccp4mg-utils/mmut/mmut_util.h A /trunk/ccp4mg-utils/mmut/splineinfo.h A /trunk/ccp4mg-utils/pygl A /trunk/ccp4mg-utils/pygl/Makefile.am A /trunk/ccp4mg-utils/pygl/atom_util.cc A /trunk/ccp4mg-utils/pygl/atom_util.h A /trunk/ccp4mg-utils/pygl/bezier.cc A /trunk/ccp4mg-utils/pygl/billboard.cc A /trunk/ccp4mg-utils/pygl/build_tree_primitives.cc A /trunk/ccp4mg-utils/pygl/catmull.cc A /trunk/ccp4mg-utils/pygl/catmull.h A /trunk/ccp4mg-utils/pygl/cbuild.h A /trunk/ccp4mg-utils/pygl/cdisplayobject.cc A /trunk/ccp4mg-utils/pygl/cdisplayobject.h A /trunk/ccp4mg-utils/pygl/cprimitive.cc A /trunk/ccp4mg-utils/pygl/cprimitive.h A /trunk/ccp4mg-utils/pygl/font_info.cc A /trunk/ccp4mg-utils/pygl/font_info.h A /trunk/ccp4mg-utils/pygl/font_util.cc A /trunk/ccp4mg-utils/pygl/font_util.h A /trunk/ccp4mg-utils/pygl/freetype_dl.c A /trunk/ccp4mg-utils/pygl/freetype_dl.h A /trunk/ccp4mg-utils/pygl/freetype_font.cc A /trunk/ccp4mg-utils/pygl/freetype_font.h A /trunk/ccp4mg-utils/pygl/help.cc A /trunk/ccp4mg-utils/pygl/help.h A /trunk/ccp4mg-utils/pygl/lincrv.cc A /trunk/ccp4mg-utils/pygl/lincrv.h A /trunk/ccp4mg-utils/pygl/psutil.cc A /trunk/ccp4mg-utils/pygl/psutil.h A /trunk/ccp4mg-utils/pygl/qt-text.cc A /trunk/ccp4mg-utils/pygl/qt-text.cc.orig A /trunk/ccp4mg-utils/pygl/rgbreps.cc A /trunk/ccp4mg-utils/pygl/rgbreps.h A /trunk/ccp4mg-utils/pygl/sphere.cc A /trunk/ccp4mg-utils/pygl/sphere.h A /trunk/ccp4mg-utils/pygl/sphere_0.h A /trunk/ccp4mg-utils/pygl/sphere_1.h A /trunk/ccp4mg-utils/pygl/sphere_2.h A /trunk/ccp4mg-utils/pygl/sphere_3.h A /trunk/ccp4mg-utils/pygl/sphere_4.h A /trunk/ccp4mg-utils/pygl/sphere_arrays.h A /trunk/ccp4mg-utils/pygl/splineset.cc A /trunk/ccp4mg-utils/pygl/subdivide.cc A /trunk/ccp4mg-utils/pygl/subdivide.h A /trunk/ccp4mg-utils/pygl/symmetry.cc A /trunk/ccp4mg-utils/pygl/symmetry.h A /trunk/ccp4mg-utils/pygl/text.cc A /trunk/ccp4mg-utils/pygl/texture.cc A /trunk/ccp4mg-utils/pygl/texture.h A /trunk/ccp4mg-utils/pygl/win_font.cc A /trunk/ccp4mg-utils/pygl/win_font.h A /trunk/ccp4mg-utils/pygl/x11_font.cc A /trunk/ccp4mg-utils/pygl/x11_font.h A /trunk/ccp4mg-utils/pygl/zsortps.cc A /trunk/ccp4mg-utils/util A /trunk/ccp4mg-utils/util/CParamsManager.cc A /trunk/ccp4mg-utils/util/CParamsManager.h A /trunk/ccp4mg-utils/util/Makefile.am A /trunk/ccp4mg-utils/util/cartesian.cc A /trunk/ccp4mg-utils/util/cartesian.h A /trunk/ccp4mg-utils/util/connect.cc A /trunk/ccp4mg-utils/util/connect.h A /trunk/ccp4mg-utils/util/geomutil.cc A /trunk/ccp4mg-utils/util/geomutil.h A /trunk/ccp4mg-utils/util/matrix.cc A /trunk/ccp4mg-utils/util/matrix.h A /trunk/ccp4mg-utils/util/mginterrupt.cc A /trunk/ccp4mg-utils/util/mginterrupt.h A /trunk/ccp4mg-utils/util/mgtree.cc A /trunk/ccp4mg-utils/util/mgtree.h A /trunk/ccp4mg-utils/util/mgutil.cc A /trunk/ccp4mg-utils/util/mgutil.h A /trunk/ccp4mg-utils/util/plane.cc A /trunk/ccp4mg-utils/util/plane.h A /trunk/ccp4mg-utils/util/quat.cc A /trunk/ccp4mg-utils/util/quat.h A /trunk/ccp4mg-utils/util/redirect.cc A /trunk/ccp4mg-utils/util/redirect.h A /trunk/ccp4mg-utils/util/volume.cc A /trunk/ccp4mg-utils/util/volume.h M /trunk/configure.in M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/python/coot_utils.py M /trunk/sequence-view/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.h make_residue_spec for python simple ribbons: added ccp4mg-utils/mmut util pygl ------------------------------------------------------------------------ r1716 | b.lohkamp | 2008-12-24 14:03:39 +0000 (Wed, 24 Dec 2008) | 4 lines Changed paths: M /trunk/python/gap.py M /trunk/src/c-interface-build.cc fix GTK1 refmac (e.g. run_refmac_mtz_file_radiobutton) fix GTK1 fit loop bug (mutate_sequence_use_ramachandran_restraints_checkbutton) fixed python loop GUI bug (GUI only shown if more than 1 loop candidates) ------------------------------------------------------------------------ r1715 | pemsley | 2008-12-19 19:54:47 +0000 (Fri, 19 Dec 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Bye bye F8 builds. ------------------------------------------------------------------------ r1714 | kevin.cowtan | 2008-12-19 16:29:19 +0000 (Fri, 19 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Remove redundent arguments (again) ------------------------------------------------------------------------ r1713 | kevin.cowtan | 2008-12-19 09:59:44 +0000 (Fri, 19 Dec 2008) | 3 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Update the fragment joining code to extend the fragments before joining, in order to join fragments which don't quite meet. ------------------------------------------------------------------------ r1712 | pemsley | 2008-12-19 09:57:52 +0000 (Fri, 19 Dec 2008) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/testing.cc Better restraints (link) searching. glycosidic linkages better now. link_infos_are_glycosidic_p() function added. matching_chem_link() returns a vector. ------------------------------------------------------------------------ r1711 | kevin.cowtan | 2008-12-19 09:36:13 +0000 (Fri, 19 Dec 2008) | 4 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Refactor classes to allow efficient threading of helix and strand searches. (A more aggressive approach to threading would involve splitting the translation search - this would be useful for >2 CPUs. Consider for later.) ------------------------------------------------------------------------ r1710 | pemsley | 2008-12-18 22:52:57 +0000 (Thu, 18 Dec 2008) | 14 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface-scm.hh M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Add scm util function to make a residue_spec from a SCM representation. Add new function refine_residues_vec, which calls generate_molecule_and_refine(). Add a make_moving_atoms_asc() function that takes a vector of residues. Add function create_mmdb_manager_from_res_vector(). Add c-interface.h function that exercises these functions. Rewrite closest_approach() so that it uses simple-minded atom by atom test for the residue comparison, not SeekContacts() which gave 0 contacts for reasons I didn't understand. Remove the restraints_container destructor delete [] atom when using a residue vector (it was needed because last_residues does a shallow copy of the restriants). Chop out some features in the rel-todo - now more sane number of items. ------------------------------------------------------------------------ r1709 | kevin.cowtan | 2008-12-17 14:55:28 +0000 (Wed, 17 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Join overlapped secondary structure elements where possible. ------------------------------------------------------------------------ r1708 | kevin.cowtan | 2008-12-16 17:18:49 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Further fast ss find cleanups. ------------------------------------------------------------------------ r1707 | kevin.cowtan | 2008-12-16 16:59:27 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Remove redundent args to SSfind::prep_results ------------------------------------------------------------------------ r1706 | kevin.cowtan | 2008-12-16 15:14:53 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Update fast ss sreach code to allow even faster search within a limited radius of the current rotation centre. ------------------------------------------------------------------------ r1705 | pemsley | 2008-12-16 14:30:31 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo Predicates should return booleans. ------------------------------------------------------------------------ r1704 | pemsley | 2008-12-16 13:53:05 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/burn-up/new-graph.py Small formatting tweaks. ------------------------------------------------------------------------ r1703 | pemsley | 2008-12-16 13:39:50 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: A /trunk/burn-up/new-burn-point.sh (from /trunk/burn-up/new-burn.sh:1699) D /trunk/burn-up/new-burn.sh M /trunk/burn-up/new-graph.py Rename to new-burn-point (it simply adds a point to the table) Take off star mark for done data points. ------------------------------------------------------------------------ r1702 | kevin.cowtan | 2008-12-16 13:36:48 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix the name of the 'Strands' molecule. ------------------------------------------------------------------------ r1701 | pemsley | 2008-12-16 13:15:51 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: A /trunk/rel-todo Add release todo notes. ------------------------------------------------------------------------ r1700 | pemsley | 2008-12-16 12:48:49 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: A /trunk/burn-up/new-graph.py Add the PyChart script to make the burn-up png. ------------------------------------------------------------------------ r1699 | pemsley | 2008-12-16 12:23:51 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: A /trunk/burn-up A /trunk/burn-up/burn-up.tab (from /trunk/burn-up.tab:1698) A /trunk/burn-up/new-burn.sh (from /trunk/new-burn.sh:1698) A /trunk/burn-up/process-rel-todo.awk (from /trunk/process-rel-todo.awk:1698) D /trunk/burn-up.tab D /trunk/new-burn.sh D /trunk/process-rel-todo.awk Move burn-up stuff to a new sub-dir. ------------------------------------------------------------------------ r1698 | pemsley | 2008-12-16 11:09:40 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/fast-ss-search.cc A newer compiler picks up syntax errors. ------------------------------------------------------------------------ r1697 | kevin.cowtan | 2008-12-16 10:09:56 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add control files for fast secondary stucture find. ------------------------------------------------------------------------ r1696 | pemsley | 2008-12-16 10:03:52 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: A /trunk/burn-up.tab A /trunk/new-burn.sh A /trunk/process-rel-todo.awk Add files for burnup chart - burn-up.tab is the actual table. Run new-burn.sh to generate a new line. ------------------------------------------------------------------------ r1695 | kevin.cowtan | 2008-12-16 10:02:09 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: M /trunk/ligand/Makefile.am M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Updated fast secondard structure finding code. Include them in the build again with Makefile.am ------------------------------------------------------------------------ r1694 | pemsley | 2008-12-16 01:20:43 +0000 (Tue, 16 Dec 2008) | 4 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-mutate.cc Change the recentre check button on reading a coordinates file to an option menu (currently of 3 choice, the last and new one being "move molecule here"). Kevin M. ------------------------------------------------------------------------ r1693 | pemsley | 2008-12-16 01:15:46 +0000 (Tue, 16 Dec 2008) | 6 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/testing.cc M /trunk/src/testing.hh New restraints handling - uses a vector of residues and refactors much restraints code to handle this and conventional/linear residue selection. Add a distance check for peptide linking. Add tests for new restraints constructor. ------------------------------------------------------------------------ r1692 | pemsley | 2008-12-16 01:11:07 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/configure.in Convert to 0.6 pre-release ------------------------------------------------------------------------ r1691 | pemsley | 2008-12-15 20:48:44 +0000 (Mon, 15 Dec 2008) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade A /trunk/pixmaps/coot-0.5.1.xpm A /trunk/pixmaps/coot-0.5.2.xpm M /trunk/python/coot_gui.py M /trunk/scheme/coot-gui.scm M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Release 0.5.2 - fix Shift label atom problem. ------------------------------------------------------------------------ r1690 | pemsley | 2008-12-15 15:29:57 +0000 (Mon, 15 Dec 2008) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Release 0.5.1. ------------------------------------------------------------------------ r1689 | pemsley | 2008-12-15 13:59:58 +0000 (Mon, 15 Dec 2008) | 7 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ligand/ideal-rna.cc M /trunk/ligand/ideal-rna.hh M /trunk/src/c-interface-gui.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/main.cc M /trunk/standard-residues.pdb Fix up ideal B form DNA by adding O2*. Change reference nucleotide for ideal B-form DNA. Update documentation for nvidia graphics. Remove some Go To Atom debugging. Dont show citation notice by default. Update dnotes and release notes. ------------------------------------------------------------------------ r1688 | pemsley | 2008-12-15 13:55:43 +0000 (Mon, 15 Dec 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Tidy up superpose ligands dialog, add handling of RTop not found in overlay-my-ligands. ------------------------------------------------------------------------ r1687 | b.lohkamp | 2008-12-15 10:16:53 +0000 (Mon, 15 Dec 2008) | 1 line Changed paths: M /trunk/scheme/extensions.scm fix typo in superpose ligand in extensions ------------------------------------------------------------------------ r1686 | b.lohkamp | 2008-12-15 09:57:29 +0000 (Mon, 15 Dec 2008) | 1 line Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm ligand superpose in extensions (py and scm) ------------------------------------------------------------------------ r1685 | kevin.cowtan | 2008-12-13 09:15:19 +0000 (Sat, 13 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/Makefile.am Revert changes to Makefile.am until after 0.5.1 ------------------------------------------------------------------------ r1684 | pemsley | 2008-12-12 18:10:16 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/TODO Update TODO. ------------------------------------------------------------------------ r1683 | kevin.cowtan | 2008-12-12 16:37:25 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/Makefile.am A /trunk/ligand/fast-ss-search.cc A /trunk/ligand/fast-ss-search.hh Add files for fast secondary structure search. ------------------------------------------------------------------------ r1682 | b.lohkamp | 2008-12-12 14:26:23 +0000 (Fri, 12 Dec 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/scheme/coot-gui.scm ligand overlay for python incl. GUI (for py and scm) ------------------------------------------------------------------------ r1681 | pemsley | 2008-12-12 13:48:40 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-defines.cc Remove rotamer debugging code. ------------------------------------------------------------------------ r1680 | pemsley | 2008-12-12 13:46:48 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/doc/crib-sheet.tex M /trunk/doc/tutorial-2.tex M /trunk/doc/user-manual.texi Update docs for Go To Residue by keyboarding. ------------------------------------------------------------------------ r1679 | pemsley | 2008-12-11 22:03:18 +0000 (Thu, 11 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Remove debugging from Ball and Sticking. ------------------------------------------------------------------------ r1678 | pemsley | 2008-12-11 22:01:57 +0000 (Thu, 11 Dec 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Make ball and stick representations move when the model moves. Stop also making Fat Bonds when making ball and sticks. ------------------------------------------------------------------------ r1677 | pemsley | 2008-12-11 17:24:59 +0000 (Thu, 11 Dec 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Rewrite reset_view(). It works correctly and relative to molecule size now. size_of_molecule() function typo fixed. Go To Atom dialog action reworked when new molecule added/created. On destroy geometry dialog, NULL the stored widget pointer. ------------------------------------------------------------------------ r1676 | pemsley | 2008-12-10 23:31:33 +0000 (Wed, 10 Dec 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-state.cc Use wrapped_create_geometry_dialog so that we don't crash on trying to open 2 of them. ------------------------------------------------------------------------ r1675 | pemsley | 2008-12-10 23:29:11 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/gap.scm Fix up loop fitting (fit-gap). ------------------------------------------------------------------------ r1674 | pemsley | 2008-12-10 18:18:18 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Document overlay-my-ligands. ------------------------------------------------------------------------ r1673 | pemsley | 2008-12-10 18:15:50 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add overlay-my-ligands function. ------------------------------------------------------------------------ r1672 | pemsley | 2008-12-10 18:08:58 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Fix up transform-coords-mol. ------------------------------------------------------------------------ r1671 | b.lohkamp | 2008-12-10 13:05:26 +0000 (Wed, 10 Dec 2008) | 3 lines Changed paths: M /trunk/python/extensions.py M /trunk/python/ncs.py M /trunk/python/unittest_extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/07_ncs.py M /trunk/scheme/extensions.scm extensions: surfaces for python ans fix scheme fix and update manual_ncs_ghosts and ncs tests ------------------------------------------------------------------------ r1670 | pemsley | 2008-12-10 09:58:49 +0000 (Wed, 10 Dec 2008) | 6 lines Changed paths: M /trunk/scheme/fitting.scm The Rama improvement stepped refine was not working properly, it had only one active residue at a time. This is because range-step was being incorrectly calculated. It should be 1 when res-step is 1. I've corrected that now (by fixing the calculation of step-inter) and Rama plot improvement is better. ------------------------------------------------------------------------ r1669 | b.lohkamp | 2008-12-10 09:00:37 +0000 (Wed, 10 Dec 2008) | 1 line Changed paths: M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h more windows jiggery fixes (when using Guile) ------------------------------------------------------------------------ r1668 | pemsley | 2008-12-10 01:39:35 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Simple surfaces gui added to Extensions -> Representations. ------------------------------------------------------------------------ r1667 | pemsley | 2008-12-10 00:53:36 +0000 (Wed, 10 Dec 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Fix up the build-log files for pythonic builds - still needs build-in-progress separated out. ------------------------------------------------------------------------ r1666 | pemsley | 2008-12-10 00:17:15 +0000 (Wed, 10 Dec 2008) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/07-ncs.scm M /trunk/scheme/ncs.scm Fix up manual-ncs-ghosts, no longer hard code in "A" as the master chain id. Add function ncs-master-chain-id. Add a test for correct NCS chain-ids after a manual-ncs-ghosts usage. booleanize the member tests in utils. Update residues_near_residue to work with a radius of 0. ------------------------------------------------------------------------ r1665 | pemsley | 2008-12-10 00:09:23 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc A tidy up of the ncs_ghost_chains() function - nothing new. ------------------------------------------------------------------------ r1664 | b.lohkamp | 2008-12-09 16:49:27 +0000 (Tue, 09 Dec 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ligand/test-ligand.cc M /trunk/python/extensions.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc NCS uses LSQ by default now etxra fast option for LSQ (every 2nd CA) in extensions (guile & python) ------------------------------------------------------------------------ r1663 | b.lohkamp | 2008-12-09 12:42:22 +0000 (Tue, 09 Dec 2008) | 1 line Changed paths: M /trunk/compat/Makefile.am M /trunk/compat/coot-sysdep.h fix windows pokery by including coot-sysdep.h ------------------------------------------------------------------------ r1662 | b.lohkamp | 2008-12-09 10:59:17 +0000 (Tue, 09 Dec 2008) | 1 line Changed paths: A /trunk/compat/coot-sysdep.h M /trunk/coords/Makefile.am M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-utils.cc M /trunk/geometry/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ligand/chi-angles.cc M /trunk/ligand/monomer-utils.cc M /trunk/ligand/rotamer.cc M /trunk/mini-mol/Makefile.am M /trunk/mini-mol/mini-mol.cc M /trunk/skeleton/BuildCas.cc M /trunk/skeleton/Makefile.am M /trunk/src/c-interface-mmdb.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc clean up windows magic jiggery ------------------------------------------------------------------------ r1661 | b.lohkamp | 2008-12-08 13:28:59 +0000 (Mon, 08 Dec 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-ncs.cc LSQ option for NCS matrix detection (in extensions for scheme and python) LSQ matching for poly-nucleotides (CA = P; main chain = P + O & ribose) loading of python modules in extra dirs (COOT_PYTHON_EXTRA_DIRS) fix for preferences font colours ------------------------------------------------------------------------ r1660 | b.lohkamp | 2008-12-08 09:54:29 +0000 (Mon, 08 Dec 2008) | 1 line Changed paths: M /trunk/src/c-interface-info.cc console highlighting and colouring for Windows Dos shell ------------------------------------------------------------------------ r1659 | pemsley | 2008-12-06 17:56:19 +0000 (Sat, 06 Dec 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Split make_monomer_restraints() by using make_monomer_restraints_by_residue(). ------------------------------------------------------------------------ r1658 | pemsley | 2008-12-06 17:08:55 +0000 (Sat, 06 Dec 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/testing.cc M /trunk/src/testing.hh Add a CResidue * vector restraints container constructor. Add the start of a test for refinement using this constructor. ------------------------------------------------------------------------ r1657 | pemsley | 2008-12-06 17:06:43 +0000 (Sat, 06 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/helix-placement.cc comment out debugging. ------------------------------------------------------------------------ r1656 | pemsley | 2008-12-06 15:18:04 +0000 (Sat, 06 Dec 2008) | 6 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-modelling.cc The last item in the monomer type chooser is now the active item. (char *) chain_id cleanup. matches_comp_ids_and_groups now returns a flag to say that the residues need to be order swapped to match. Used in find_link_type_rigourous(). ------------------------------------------------------------------------ r1655 | pemsley | 2008-12-06 15:11:27 +0000 (Sat, 06 Dec 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex png -> ps. ------------------------------------------------------------------------ r1654 | pemsley | 2008-12-05 14:36:03 +0000 (Fri, 05 Dec 2008) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc Add a bit of protection for rotate_chi, don't do anything if not in rotate_chi mode. ------------------------------------------------------------------------ r1653 | pemsley | 2008-12-05 13:43:05 +0000 (Fri, 05 Dec 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add to the scripting layer rotate_chi() function - to be activated by a PowerMate (for example) in due course. ------------------------------------------------------------------------ r1652 | pemsley | 2008-12-05 00:15:16 +0000 (Fri, 05 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm More elegant formatting of the residue-density-fit-scale-factor text. ------------------------------------------------------------------------ r1651 | b.lohkamp | 2008-12-04 10:15:09 +0000 (Thu, 04 Dec 2008) | 5 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/07_ncs.py M /trunk/scheme/extensions.scm buttonize the python key bindings density graph weight GUI in extensions picks up the current weight (scm & py) python tests: moved NCS map test from 01_pdb_mtz.py to 07_ncs.py updated dynamically_transformed maps in tests ------------------------------------------------------------------------ r1650 | pemsley | 2008-12-04 08:44:30 +0000 (Thu, 04 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/ligand.cc Remove inadvertent addition of ligand fitting debugging code. ------------------------------------------------------------------------ r1649 | pemsley | 2008-12-03 14:44:39 +0000 (Wed, 03 Dec 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/07-ncs.scm M /trunk/ideal/simple-restraint.cc Move NCS test from 01-pdb+mtz. Better logic for the fixed atom in link restraints. ------------------------------------------------------------------------ r1648 | pemsley | 2008-12-03 12:48:02 +0000 (Wed, 03 Dec 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/07-ncs.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h dynamically_transform_maps now takes an extra arg, flag to tell whether or not to try to overwrite existing maps of the same name. Test for dynamically_transform_maps(). ------------------------------------------------------------------------ r1647 | pemsley | 2008-12-03 06:23:21 +0000 (Wed, 03 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm buttonize the scheme+python keybindings (using alignment). ------------------------------------------------------------------------ r1646 | b.lohkamp | 2008-12-02 19:01:31 +0000 (Tue, 02 Dec 2008) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/ncs.py M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h update of python scripts (fix shelx refine extension, ncs, ...) python function for find_terminal_residue_type set_display_maps... for windows stereo (actually previous commit, r1645) ------------------------------------------------------------------------ r1645 | b.lohkamp | 2008-12-02 14:32:55 +0000 (Tue, 02 Dec 2008) | 1 line Changed paths: M /trunk/build-it-win M /trunk/src/c-interface.cc update Windows build script; fix python shelx refine GUI ------------------------------------------------------------------------ r1644 | pemsley | 2008-12-02 13:45:39 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/src/main.cc Add Stuart's suggestion for python signal handlers. ------------------------------------------------------------------------ r1643 | pemsley | 2008-12-02 13:44:52 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc Remove debugging. ------------------------------------------------------------------------ r1642 | pemsley | 2008-12-02 13:43:55 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/doc/tutorial-2.tex Note to add 4mer-XYS to tutorial-2.tex at some stage. ------------------------------------------------------------------------ r1641 | pemsley | 2008-12-02 13:43:10 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/ligand.cc Reformatting. ------------------------------------------------------------------------ r1640 | pemsley | 2008-12-02 08:16:07 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Use ps files in tutorial, not pngs (which don't work on bubbles). ------------------------------------------------------------------------ r1639 | pemsley | 2008-12-02 07:49:54 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for NCS Ghosts by Residue Range. ------------------------------------------------------------------------ r1638 | pemsley | 2008-12-02 07:40:58 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a GUI for manual-ncs-ghosts - called "NCS Ghosts by Residue Range...". ------------------------------------------------------------------------ r1637 | pemsley | 2008-12-02 01:34:51 +0000 (Tue, 02 Dec 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc Add a operator<< for a chem_link. chem_link should match groups and comp_ids. ------------------------------------------------------------------------ r1636 | pemsley | 2008-12-02 00:53:28 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc In closest_atom() check the chain_id if set. ------------------------------------------------------------------------ r1635 | pemsley | 2008-12-01 23:11:18 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/src/graphics-info.cc In closest_atom() do no to consider molecules that are not displayed. ------------------------------------------------------------------------ r1634 | pemsley | 2008-12-01 19:06:34 +0000 (Mon, 01 Dec 2008) | 9 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Move active_atom_spec() to graphics_info. Adjust closest_atom() to take a chain-id. Add get_atom, which uses closest_atom(). Add internals for for key presses to add to graphics_info_t::go_to_residue_keyboarding_string Add related static bool in_go_to_residue_keyboarding_mode and apply_go_to_residue_keyboading_string(); Utility functions is_number() and is_letter() for given chars. ------------------------------------------------------------------------ r1633 | pemsley | 2008-12-01 15:02:14 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Add a return value to matching_chem_link() and throw an error if not found. ------------------------------------------------------------------------ r1632 | pemsley | 2008-12-01 14:14:57 +0000 (Mon, 01 Dec 2008) | 14 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/scheme/ncs.scm Rename manual-ncs-ghosts as single-manual-ncs-ghost. Introduce new function manual-ncs-ghosts which handles several ghosts chains. closest_approach() function added to utils - function is given 2 residues and returns the closest 2 atoms of those residues. Enhance chem_link class in dictionary. Allow the searching of the chem_links given residue groups. Introduce bonded_pair (of residues) and a container class for them. Add rigourous residue linking - not actived yet, because there is no way to pass a non-linear set of residues to the make_restraints() function. Allow residues that are close in residue index to be bonded (draw). Allow residues that are close in residue index to be restrainted as a peptide bond. ------------------------------------------------------------------------ r1631 | pemsley | 2008-12-01 13:10:48 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-surface.cc Handle the lights better when drawing a surface. ------------------------------------------------------------------------ r1630 | pemsley | 2008-12-01 12:45:53 +0000 (Mon, 01 Dec 2008) | 4 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/ppmutil.cc M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXSpace.cpp Fixes for G++ 4.3.2 on intrepid. Make the keyboard zoom a bit smooth. Bump the version of GMP in build-it-gtk-simple. ------------------------------------------------------------------------ r1629 | pemsley | 2008-12-01 01:06:38 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-fasta.cc Protection parentheses around fasta test logical operators. ------------------------------------------------------------------------ r1628 | pemsley | 2008-11-30 18:34:24 +0000 (Sun, 30 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix build_type typo. ------------------------------------------------------------------------ r1627 | pemsley | 2008-11-28 18:37:38 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Trivial formatting. ------------------------------------------------------------------------ r1626 | pemsley | 2008-11-28 15:41:59 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add protection for map_is_displayed(). ------------------------------------------------------------------------ r1625 | pemsley | 2008-11-28 15:29:29 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Restore F8 to the build status page for now. ------------------------------------------------------------------------ r1624 | pemsley | 2008-11-28 12:14:31 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix output log file for gtk2. ------------------------------------------------------------------------ r1623 | pemsley | 2008-11-27 08:08:22 +0000 (Thu, 27 Nov 2008) | 2 lines Changed paths: M /trunk/build-it Make file_list in post_install_slim python-dependent, like the gtk2 version. ------------------------------------------------------------------------ r1622 | pemsley | 2008-11-26 17:56:54 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/python/Makefile.am Remove Makefile.am from EXTRA_DIST. ------------------------------------------------------------------------ r1621 | pemsley | 2008-11-26 13:30:08 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Add some protection to the index in undos. ------------------------------------------------------------------------ r1620 | pemsley | 2008-11-26 13:28:51 +0000 (Wed, 26 Nov 2008) | 3 lines Changed paths: M /trunk/scheme/gap.scm Fix up fit-gap so that the sequence/rama-flag need not be passed - as it used to be. ------------------------------------------------------------------------ r1619 | pemsley | 2008-11-26 13:27:46 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Allow a link restraint between residues that have neighbouring indexes. ------------------------------------------------------------------------ r1618 | pemsley | 2008-11-26 13:26:17 +0000 (Wed, 26 Nov 2008) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc Allow the bonding of close atoms that have residues with neighbouring indexes. ------------------------------------------------------------------------ r1617 | b.lohkamp | 2008-11-26 12:00:54 +0000 (Wed, 26 Nov 2008) | 1 line Changed paths: M /trunk/build-it-win M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ligand/chi-angles.cc M /trunk/ligand/monomer-utils.cc M /trunk/ligand/rotamer.cc M /trunk/macros/clipper.m4 M /trunk/mini-mol/mini-mol.cc M /trunk/skeleton/BuildCas.cc make WinCoot clipper 2.1 compliant (incl threading) ------------------------------------------------------------------------ r1616 | pemsley | 2008-11-26 08:37:02 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Quote the argument to info-dialog for the history. ------------------------------------------------------------------------ r1615 | pemsley | 2008-11-24 19:57:37 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1614 | pemsley | 2008-11-24 19:57:14 +0000 (Mon, 24 Nov 2008) | 3 lines Changed paths: A /trunk/geometry/chiral-notes.txt M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc Add dictionary restraints of type "both" - but don't use them to make a restraint. ------------------------------------------------------------------------ r1613 | pemsley | 2008-11-24 19:55:03 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Test for greg using full path to guile. ------------------------------------------------------------------------ r1612 | pemsley | 2008-11-24 18:25:11 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Comment out Pukka Puckers for now. ------------------------------------------------------------------------ r1611 | pemsley | 2008-11-24 15:35:28 +0000 (Mon, 24 Nov 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh Remove debugging from restraints editor. Add function size_of_molecule(). Update dnotes. ------------------------------------------------------------------------ r1610 | pemsley | 2008-11-24 13:58:08 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Get ssh and tar file move in the right order. ------------------------------------------------------------------------ r1609 | pemsley | 2008-11-24 13:38:18 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add debugging info for the ssh_copy. ------------------------------------------------------------------------ r1608 | pemsley | 2008-11-24 13:28:03 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Sort out python_version and pver usage in post_install_slim. ------------------------------------------------------------------------ r1607 | pemsley | 2008-11-24 12:58:42 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add in gtk2 tar for tar files of gtk2 builds. ------------------------------------------------------------------------ r1606 | pemsley | 2008-11-24 12:23:37 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add find-terminal-residue-type for snarfing. ------------------------------------------------------------------------ r1605 | pemsley | 2008-11-24 12:17:27 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/macros/clipper.m4 Add -lpthread to clipper libs in the macro. ------------------------------------------------------------------------ r1604 | pemsley | 2008-11-24 07:45:36 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix typo in holding tar handling. ------------------------------------------------------------------------ r1603 | pemsley | 2008-11-24 07:13:58 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple link the greg-tests dir in second-test untar dir. ------------------------------------------------------------------------ r1602 | pemsley | 2008-11-24 00:18:15 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix dir for untar/test ------------------------------------------------------------------------ r1601 | pemsley | 2008-11-24 00:13:35 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple fix typo in untaring tar file for test. ------------------------------------------------------------------------ r1600 | pemsley | 2008-11-23 23:56:42 +0000 (Sun, 23 Nov 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Yet more adjustment of the second test - use the holding_tar_file, pipe the test output. ------------------------------------------------------------------------ r1599 | pemsley | 2008-11-23 23:36:04 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple make a holding directory for tar file for pre-release case. ------------------------------------------------------------------------ r1598 | pemsley | 2008-11-23 17:56:39 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it Fix the gtk1 vs gtk2 problem for the slim tar file. ------------------------------------------------------------------------ r1597 | pemsley | 2008-11-23 17:35:28 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it make holding dir in gtk1 build. ------------------------------------------------------------------------ r1596 | pemsley | 2008-11-23 16:07:55 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple More typos in build-it scripts for second test. ------------------------------------------------------------------------ r1595 | pemsley | 2008-11-23 15:17:44 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it Fix typo at the end of the script. ------------------------------------------------------------------------ r1594 | pemsley | 2008-11-23 14:14:33 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix typo. ------------------------------------------------------------------------ r1593 | pemsley | 2008-11-23 12:29:38 +0000 (Sun, 23 Nov 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Add in a second test - for the tar file. If that fails don't move the binary tar from holding dir. ------------------------------------------------------------------------ r1592 | pemsley | 2008-11-23 11:50:51 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Remove python fedora 8 build report too. ------------------------------------------------------------------------ r1591 | pemsley | 2008-11-23 11:49:18 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Remove Fedora 8 from the build. There is something wrong with the build host. ------------------------------------------------------------------------ r1590 | pemsley | 2008-11-22 19:15:57 +0000 (Sat, 22 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1589 | pemsley | 2008-11-22 07:41:43 +0000 (Sat, 22 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use clipper-2.1, extra tweaks. ------------------------------------------------------------------------ r1588 | pemsley | 2008-11-22 07:19:39 +0000 (Sat, 22 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Try use clipper-2.1 ------------------------------------------------------------------------ r1587 | pemsley | 2008-11-21 12:20:03 +0000 (Fri, 21 Nov 2008) | 4 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Remove l keypress to label atom on click, Add l keypress to label atom closest to screen centre. Rename graphics_info_t::l_is_pressed to graphics_info_t::shift_is_pressed. ------------------------------------------------------------------------ r1586 | pemsley | 2008-11-21 08:14:34 +0000 (Fri, 21 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo. ------------------------------------------------------------------------ r1585 | pemsley | 2008-11-21 08:04:30 +0000 (Fri, 21 Nov 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple swig 1.3.34 is OK for 32 bit systems, I think. Don't halt the build if architecture is not x86_64. ------------------------------------------------------------------------ r1584 | pemsley | 2008-11-20 15:51:09 +0000 (Thu, 20 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r1583 | pemsley | 2008-11-20 15:11:16 +0000 (Thu, 20 Nov 2008) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/ligand/monomer-utils.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/rotamer.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Add insertion codes into deep_copy_residue() and use SetResID() on copied residues. Fixes problems with rotamers on residues with insertion codes. Add a test for rotamers using 3hfl. ------------------------------------------------------------------------ r1582 | pemsley | 2008-11-19 21:05:42 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add CentOS 64 bit builts. ------------------------------------------------------------------------ r1581 | pemsley | 2008-11-19 21:04:59 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes Tweak for 64 bit builds of coot - Use -O rather rather than -O2. ------------------------------------------------------------------------ r1580 | pemsley | 2008-11-19 21:02:03 +0000 (Wed, 19 Nov 2008) | 3 lines Changed paths: M /trunk/src/graphics-info.cc If the umol does not have modifications, reset undo_molecule regardless of whether or not graphics are being used. ------------------------------------------------------------------------ r1579 | pemsley | 2008-11-19 11:19:58 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1578 | pemsley | 2008-11-18 23:02:44 +0000 (Tue, 18 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use the ccp4 libs underlay. ------------------------------------------------------------------------ r1577 | pemsley | 2008-11-17 20:09:54 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/junk.cc Fix the re-scaling issue for rotamers on updating the molecule [JED]. Add a flash of the picked atom when in Ctrl-pick vs Ctrl-drag mode. ------------------------------------------------------------------------ r1576 | pemsley | 2008-11-17 12:59:21 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /trunk/ligand/helix-placement.cc M /trunk/ligand/rotamer-tables.cc Add debugging (for map R 3 2 issue) in helix placement. Remove debugging in rotamer tables (self test). ------------------------------------------------------------------------ r1575 | pemsley | 2008-11-16 02:55:08 +0000 (Sun, 16 Nov 2008) | 3 lines Changed paths: M /trunk/ideal/pepflip.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc Make sure that a pepflip flips the H on the N too - fixed the atom names of the C and the O - how did it ever work before? ------------------------------------------------------------------------ r1574 | pemsley | 2008-11-15 20:34:58 +0000 (Sat, 15 Nov 2008) | 3 lines Changed paths: M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Add test for add_atom function. Rename add_cb_to_terminal_res() to add_side_chain_to_terminal_res(), which is more like what it does. ------------------------------------------------------------------------ r1573 | pemsley | 2008-11-15 20:32:42 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Reformatting of long line. ------------------------------------------------------------------------ r1572 | pemsley | 2008-11-15 20:31:56 +0000 (Sat, 15 Nov 2008) | 3 lines Changed paths: M /trunk/src/callbacks.c M /trunk/src/positioned-widgets.h set transient geometry dialog in on_distances_and_angles1_activate() by using COOT_UNDEFINED_WINDOW. ------------------------------------------------------------------------ r1571 | pemsley | 2008-11-15 20:29:52 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add add_atom function, which adds an atom to a CResidue. ------------------------------------------------------------------------ r1570 | pemsley | 2008-11-15 17:24:30 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes sync dnotes. ------------------------------------------------------------------------ r1569 | pemsley | 2008-11-15 16:56:02 +0000 (Sat, 15 Nov 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add get_monomer_from_dictionary() function, that gets molecules from the PDB's Chemical Component Library (no restraints). Now uses move_molecule_to_screen_centre_internal. Mostly additions to protein-geometry to add the reading of chem_comp info without using a loop. ------------------------------------------------------------------------ r1568 | pemsley | 2008-11-15 16:52:20 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Add some debugging - but not used. ------------------------------------------------------------------------ r1567 | pemsley | 2008-11-15 16:51:34 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Add some more debugging to with-map.cc. ------------------------------------------------------------------------ r1566 | pemsley | 2008-11-15 16:50:18 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Don't set_transient for store_geometry_dialog(). ------------------------------------------------------------------------ r1565 | pemsley | 2008-11-15 16:48:53 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm define find-aligned-residue-type as find-terminal-residue-type. ------------------------------------------------------------------------ r1564 | b.lohkamp | 2008-11-13 12:03:48 +0000 (Thu, 13 Nov 2008) | 1 line Changed paths: A /trunk/pixmaps/stop.svg M /trunk/python/coot_utils.py M /trunk/python/refmac.py refmac runs 'concurrently' in python now ------------------------------------------------------------------------ r1563 | b.lohkamp | 2008-11-12 09:06:57 +0000 (Wed, 12 Nov 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows autobuild to mmdb 1.19 ------------------------------------------------------------------------ r1562 | b.lohkamp | 2008-11-11 18:58:29 +0000 (Tue, 11 Nov 2008) | 4 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/main.cc rework small-screen detection (not neccessary to use flag any more) added two contour levels for difference maps and map colours in CCP4MG picture file ------------------------------------------------------------------------ r1561 | b.lohkamp | 2008-11-11 09:47:27 +0000 (Tue, 11 Nov 2008) | 3 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/command-line.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/main.cc test for reading/writing gz pdbs (mainly for windows) no-graphics mode protection for toolbar icons ------------------------------------------------------------------------ r1560 | pemsley | 2008-11-10 23:34:50 +0000 (Mon, 10 Nov 2008) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Some debugging of input to fft. ------------------------------------------------------------------------ r1559 | pemsley | 2008-11-10 22:42:57 +0000 (Mon, 10 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Upgrade to mmdb-1.19, get tar file from EBI. ------------------------------------------------------------------------ r1558 | pemsley | 2008-11-10 22:32:28 +0000 (Mon, 10 Nov 2008) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info.cc Change the heuristic fencepost on the number of sensible coloured lines to 512,000. That should be enough even for ribosomes. ------------------------------------------------------------------------ r1557 | b.lohkamp | 2008-11-10 19:35:29 +0000 (Mon, 10 Nov 2008) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/src/c-interface-preferences.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-preferences.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc update font colours in preferences small-screen setting automatically detected and applied enable using gzipped files for reading and writing coordinates in windows ------------------------------------------------------------------------ r1556 | pemsley | 2008-11-09 15:29:30 +0000 (Sun, 09 Nov 2008) | 5 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/graphics-info.cc M /trunk/src/pick.h When molecule is in coot::CA_BONDS_PLUS_LIGANDS allow regularize_object_bonds_box to be drawn in with do_Ca_plus_ligands_bonds() args to a bonds_box, rather than do_Ca_bonds(). Allow the torsion of ligands in CA+Ligands mode [Ingo Korndoefer]. ------------------------------------------------------------------------ r1555 | pemsley | 2008-11-09 15:26:57 +0000 (Sun, 09 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Again, don't use clipper-new-ccp4-install.patch or mmdbold. ------------------------------------------------------------------------ r1554 | pemsley | 2008-11-09 15:23:51 +0000 (Sun, 09 Nov 2008) | 2 lines Changed paths: M /trunk/scheme/mutate.scm Fix typo in args to mutate. ------------------------------------------------------------------------ r1553 | pemsley | 2008-11-09 15:22:55 +0000 (Sun, 09 Nov 2008) | 3 lines Changed paths: M /trunk/build-it Don't patch with clipper-new-ccp4-install.patch. Don't enable mmdbold with clipper. ------------------------------------------------------------------------ r1552 | pemsley | 2008-11-08 11:55:07 +0000 (Sat, 08 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Correct the mkdir of the python include dir. ------------------------------------------------------------------------ r1551 | pemsley | 2008-11-08 10:55:26 +0000 (Sat, 08 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple If no compiler then exit. ------------------------------------------------------------------------ r1550 | pemsley | 2008-11-07 23:35:55 +0000 (Fri, 07 Nov 2008) | 9 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh Fix up find-terminal-residue-type so that it can find the residue type of a residue in the middle of a chain (not just an insertion at the end - mutations are now checked also). define find-aligned-residue-type as find-terminal-residue-type. In coot-align.hh let add_mutation aand add_deletion take the chain_id too. Fix some unassigned variable usage. Yet more tweaking of the build script - don't try to remove the build status file if it is not there. ------------------------------------------------------------------------ r1549 | kevin.cowtan | 2008-11-07 13:34:58 +0000 (Fri, 07 Nov 2008) | 5 lines Changed paths: M /trunk/src/c-interface.cc More radical rewrite of auto-open-mtz. Allows for future expansion, including the use of weights in the list of standard column names. Checks for duplicate column labels, to prevent the same map being opened twice. Code duplication reduced significantly. ------------------------------------------------------------------------ r1548 | pemsley | 2008-11-06 19:28:19 +0000 (Thu, 06 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm tweak the builder info for cycle. ------------------------------------------------------------------------ r1547 | b.lohkamp | 2008-11-06 18:28:44 +0000 (Thu, 06 Nov 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/extensions.py M /trunk/scheme/extensions.scm read refmac log file for outliers in Extension (py and scm) ------------------------------------------------------------------------ r1546 | kevin.cowtan | 2008-11-06 17:16:52 +0000 (Thu, 06 Nov 2008) | 4 lines Changed paths: M /trunk/src/c-interface.cc Make auto-open MTZ open ALL maps from density modification using a list of typical column labels. We should think about what other labels we might add. ------------------------------------------------------------------------ r1545 | b.lohkamp | 2008-11-06 09:47:22 +0000 (Thu, 06 Nov 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/python/gap.py M /trunk/python/refmac.py M /trunk/python-tests/02_shelx.py M /trunk/scheme/gap.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c added 'Ramachandran Restraints' check button in fit loop GUI (GTK2) fit loop does extra loop build (no res>=6) half from N- and C-terminus (python) python test or shelx aniso U Uij in residue_info are in pdb format order ------------------------------------------------------------------------ r1544 | pemsley | 2008-11-05 10:31:59 +0000 (Wed, 05 Nov 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/02-shelx.scm M /trunk/src/c-interface-info.cc Write out the ansio Us in an atom spec if the atom has them (a list with the b_iso_equiv first). Add a greg test-case for this and previous aniso Us. ------------------------------------------------------------------------ r1543 | pemsley | 2008-11-05 10:29:03 +0000 (Wed, 05 Nov 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Fractionalize the aniso Us before writing them to the output .ins file. ------------------------------------------------------------------------ r1542 | pemsley | 2008-11-02 23:15:39 +0000 (Sun, 02 Nov 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for manual-ncs-ghosts. ------------------------------------------------------------------------ r1541 | pemsley | 2008-11-01 01:14:12 +0000 (Sat, 01 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Make the slim-dir be python-dependent. ------------------------------------------------------------------------ r1540 | pemsley | 2008-11-01 01:10:37 +0000 (Sat, 01 Nov 2008) | 2 lines Changed paths: M /trunk/build-it More adjustment of the prefix, now that we have python differentiation. ------------------------------------------------------------------------ r1539 | pemsley | 2008-11-01 01:03:27 +0000 (Sat, 01 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Adjust settings for setsuko. ------------------------------------------------------------------------ r1538 | pemsley | 2008-10-31 22:10:58 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Fix typo in ierr. ------------------------------------------------------------------------ r1537 | pemsley | 2008-10-31 17:29:34 +0000 (Fri, 31 Oct 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc Make the simple_mon_lib_chewm_comp consistent (re: desc_level) with chem_comp. ------------------------------------------------------------------------ r1536 | pemsley | 2008-10-31 16:59:09 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc If desc_level is in the cif file, extract it, otherwise set it to "None". ------------------------------------------------------------------------ r1535 | b.lohkamp | 2008-10-31 15:41:05 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/scheme/generic-objects.scm M /trunk/src/c-inner-main.c made reduce pdb v3 compliant (i.e. removed -oldpdb flag) ------------------------------------------------------------------------ r1534 | pemsley | 2008-10-31 08:33:28 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Reorder build cells and correct name for cycle. ------------------------------------------------------------------------ r1533 | pemsley | 2008-10-30 18:43:54 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple My python configuration tinkering, this time to coot's configure. ------------------------------------------------------------------------ r1532 | pemsley | 2008-10-30 14:37:30 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add Cl and Br to inpected element ids (these are mixed case). ------------------------------------------------------------------------ r1531 | b.lohkamp | 2008-10-30 11:08:56 +0000 (Thu, 30 Oct 2008) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/ligand/ligand.cc M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Add a python-representation and reorder_chain function + GUI set B-factors for new/mutated atoms to 30 (in ligands.cc as for g.default_new_atoms_b_factor) update the settings of toolbar icons menu selection Add some functions to set b-factors (python only so far) Add reset b-factor after refinement button to refinement options GUI ------------------------------------------------------------------------ r1530 | pemsley | 2008-10-30 00:41:56 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1529 | pemsley | 2008-10-30 00:41:14 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/standard-residues.pdb Add Xr residue. Not used yet. ------------------------------------------------------------------------ r1528 | pemsley | 2008-10-30 00:40:39 +0000 (Thu, 30 Oct 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Adjust install_top_dir and generic_prefix so that they are different for python pre-release builds. ------------------------------------------------------------------------ r1527 | b.lohkamp | 2008-10-29 16:12:20 +0000 (Wed, 29 Oct 2008) | 1 line Changed paths: M /trunk/build-it-win update windows build script ------------------------------------------------------------------------ r1526 | pemsley | 2008-10-29 14:46:23 +0000 (Wed, 29 Oct 2008) | 5 lines Changed paths: M /trunk/mapview.glade M /trunk/src/c-interface-superpose.cc M /trunk/src/interface.c least_squares_move_copy_checkbutton was not in gtk1 interface so refering to it crashed coot. Added protection to its use in apply_lsq_matches_by_widget and added it to the gtk1 interface. ------------------------------------------------------------------------ r1525 | b.lohkamp | 2008-10-29 09:51:19 +0000 (Wed, 29 Oct 2008) | 1 line Changed paths: M /trunk/python-tests/begin.py M /trunk/python-tests/coot_unittest.py fixed python 2.6 testing problem ------------------------------------------------------------------------ r1524 | pemsley | 2008-10-29 08:46:15 +0000 (Wed, 29 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple re-work the building of python again. ------------------------------------------------------------------------ r1523 | pemsley | 2008-10-29 08:34:17 +0000 (Wed, 29 Oct 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add scheme-representation and reorder-chains functions (so that chains are now in lexographical order) and add a simple GUI to that function. ------------------------------------------------------------------------ r1522 | pemsley | 2008-10-29 07:36:29 +0000 (Wed, 29 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Better exitting when python not correct. ------------------------------------------------------------------------ r1521 | pemsley | 2008-10-29 07:26:45 +0000 (Wed, 29 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Tinker with python version settings. Now use 2.6 in both. ------------------------------------------------------------------------ r1520 | pemsley | 2008-10-28 18:12:08 +0000 (Tue, 28 Oct 2008) | 3 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc More reworking of py_to_scm() and py_clean_internal(). If PyObject o is a function, render that as a string. ------------------------------------------------------------------------ r1519 | pemsley | 2008-10-28 18:11:13 +0000 (Tue, 28 Oct 2008) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc Relabel menu item (CA/backbone, now we do P backbone). Remove debugging. ------------------------------------------------------------------------ r1518 | b.lohkamp | 2008-10-28 16:16:23 +0000 (Tue, 28 Oct 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/cootrc.template M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/command-line.cc M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc synchronised MFR dialog and modelling toolbar moved 'Add Water' to 'Other Modelling Tools' (GTK2) model toolbar defaults to all icons added preferences to change toolbar outline ------------------------------------------------------------------------ r1517 | pemsley | 2008-10-28 07:36:01 +0000 (Tue, 28 Oct 2008) | 2 lines Changed paths: M /trunk/src/pick.cc Allow the picking of Ps in CA mode. ------------------------------------------------------------------------ r1516 | pemsley | 2008-10-28 07:35:37 +0000 (Tue, 28 Oct 2008) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Allow the P backbone mode in CA display mode. ------------------------------------------------------------------------ r1515 | pemsley | 2008-10-28 03:55:57 +0000 (Tue, 28 Oct 2008) | 2 lines Changed paths: M /trunk/Makefile.am Change cootrc to cootrc.template for EXTRA_DIST. ------------------------------------------------------------------------ r1514 | pemsley | 2008-10-28 03:51:27 +0000 (Tue, 28 Oct 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/callbacks.c M /trunk/src/gtk-manual.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/rama_plot.cc Fix up handling of the scroll group for the "Delete" button in the Display Manager. Fixes JED crash. ------------------------------------------------------------------------ r1513 | pemsley | 2008-10-27 16:52:45 +0000 (Mon, 27 Oct 2008) | 8 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/gtk-manual.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info.cc configure.in sets up commands to build cootrc. Add a command line argument to inhibit splash screen. Add a command line arg to change the splash screen (non-working, as we need to pass the splash screen widget creator the file name to the image.). The "delete molecule" button in the display control crashes coot somehow add some debugging. Start adding SBASE interface into Coot. ------------------------------------------------------------------------ r1512 | pemsley | 2008-10-27 16:48:46 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: D /trunk/cootrc A /trunk/cootrc.template (from /trunk/cootrc:1511) Move cootrc to cootrc.template, now that we can address gtk1 issues. ------------------------------------------------------------------------ r1511 | pemsley | 2008-10-27 16:48:10 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/cootrc Update cootrc - there are diffs, needs a mv to template. ------------------------------------------------------------------------ r1510 | pemsley | 2008-10-27 16:45:09 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Remove debugging. ------------------------------------------------------------------------ r1509 | pemsley | 2008-10-27 16:44:19 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Remove pukka puckers until it works properly. ------------------------------------------------------------------------ r1508 | pemsley | 2008-10-27 16:39:36 +0000 (Mon, 27 Oct 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Don't make test after the python build. Use python version 2.6 ------------------------------------------------------------------------ r1507 | pemsley | 2008-10-27 16:37:30 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/doc/tutorial-2.tex M /trunk/doc/tutorial.tex Update the tutorials. ------------------------------------------------------------------------ r1506 | pemsley | 2008-10-27 02:19:12 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1505 | b.lohkamp | 2008-10-23 22:32:15 +0100 (Thu, 23 Oct 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/cootrc A /trunk/pixmaps/edit-backbone.svg M /trunk/pixmaps/side-chain-180.svg A /trunk/pixmaps/torsion-general.svg M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/gtk2-interface.c new icons for 'Torsion General' and 'Edit Backbone Torsion' modeling toolbar and MFR dialog have same buttons now (although not all shown in toolbar by default) ------------------------------------------------------------------------ r1504 | b.lohkamp | 2008-10-23 14:47:25 +0100 (Thu, 23 Oct 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_toolbuttons.py M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/testing.cc compiles without GSL now (not sure how usefull and if it is as functional as possible refmac with input mtz file works properly now (?!) updates to refmac.py/scm to work with mtz file input ------------------------------------------------------------------------ r1503 | b.lohkamp | 2008-10-21 19:31:35 +0100 (Tue, 21 Oct 2008) | 8 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/doc/tutorial.tex M /trunk/python/refmac.py M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/support.h update tutorial with Kevin's images (GTK2) flag and some implementation of resetting of b-factors after refinement copy button for lsq fit GUI re-worked refmac GUI so that you always can take an mtz file as input (needs cleaning up, fixing of phase combination and some implementation in the scheme scripting) ------------------------------------------------------------------------ r1502 | pemsley | 2008-10-17 17:47:45 +0100 (Fri, 17 Oct 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix doc typos. ------------------------------------------------------------------------ r1501 | pemsley | 2008-10-17 13:17:33 +0100 (Fri, 17 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add in non-pythonic centOS 4 gtk2 binary. ------------------------------------------------------------------------ r1500 | b.lohkamp | 2008-10-17 10:27:18 +0100 (Fri, 17 Oct 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/doc/tutorial.tex M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/src/graphics-info.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h add GUI/assistent for a user-defined toolbutton in the toolbar menu update the tutorial to be GTK2 compliant (preferences, modeeling toolbar) fixed crash when trying to load images and no appropriate pix-buf loader was available ------------------------------------------------------------------------ r1499 | pemsley | 2008-10-15 15:28:05 +0100 (Wed, 15 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm i686 bins not i386 for ubuntu 8.04. ------------------------------------------------------------------------ r1498 | pemsley | 2008-10-15 11:30:07 +0100 (Wed, 15 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Enable imminent bragg3 build watcher. ------------------------------------------------------------------------ r1497 | pemsley | 2008-10-15 07:46:51 +0100 (Wed, 15 Oct 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Updates to test for patch before continuing. Don't look for bragg3 bins, it can't compile code yet. ------------------------------------------------------------------------ r1496 | b.lohkamp | 2008-10-13 16:13:01 +0100 (Mon, 13 Oct 2008) | 1 line Changed paths: M /trunk/scheme/refmac.scm fixed (guile) run-refmac-for-phases ------------------------------------------------------------------------ r1495 | pemsley | 2008-10-13 14:07:38 +0100 (Mon, 13 Oct 2008) | 2 lines Changed paths: M /trunk/doc/tutorial-2.tex Update tutorial-2.tex ------------------------------------------------------------------------ r1494 | pemsley | 2008-10-10 13:42:24 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Update relnotes. ------------------------------------------------------------------------ r1493 | pemsley | 2008-10-10 13:36:03 +0100 (Fri, 10 Oct 2008) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/test-read-components.cc M /trunk/src/c-interface-validate.cc Add mmdb-mmdb-long-line patch to mmdb build. Remove reference to gtk_widget_unref on baddie checked waters - fixes crash [JED]. Enable SBASE in protein geometry. Add is_directory_p() function. ------------------------------------------------------------------------ r1492 | pemsley | 2008-10-10 11:51:02 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix typo in source code build log file name. ------------------------------------------------------------------------ r1491 | pemsley | 2008-10-10 11:35:04 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add setsuko builds. ------------------------------------------------------------------------ r1490 | pemsley | 2008-10-10 11:32:01 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix typo in reading source build status. ------------------------------------------------------------------------ r1489 | b.lohkamp | 2008-10-09 15:30:40 +0100 (Thu, 09 Oct 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py conditional import gobject in coot_gui.py ------------------------------------------------------------------------ r1488 | b.lohkamp | 2008-10-09 14:44:00 +0100 (Thu, 09 Oct 2008) | 1 line Changed paths: M /trunk/python/get_ebi.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/08_utils.py python (tests) fixes and updates ------------------------------------------------------------------------ r1487 | pemsley | 2008-10-09 09:58:55 +0100 (Thu, 09 Oct 2008) | 2 lines Changed paths: M /trunk/src/c-interface.h Improve doxygen documentation for Ramachandran angles. ------------------------------------------------------------------------ r1486 | pemsley | 2008-10-09 08:36:51 +0100 (Thu, 09 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Read 2-line status from build-status/status. ------------------------------------------------------------------------ r1485 | pemsley | 2008-10-08 23:46:34 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/ligand/wiggly-ligand.cc Remove some debugging from wiggly ligands. ------------------------------------------------------------------------ r1484 | pemsley | 2008-10-08 17:19:56 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Migrate to CCP4 version 6.0.2 for testing in York. ------------------------------------------------------------------------ r1483 | pemsley | 2008-10-08 17:06:00 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm More debugging for setting of CCP4. ------------------------------------------------------------------------ r1482 | pemsley | 2008-10-08 17:04:44 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add some debugging for setting up of CCP4. ------------------------------------------------------------------------ r1481 | pemsley | 2008-10-08 14:15:49 +0100 (Wed, 08 Oct 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/src/callbacks.c Read a PART card from a shelxl file with a site occupancy factor. Clean up response handling in on_save_restraint_chooserdialog_response(). ------------------------------------------------------------------------ r1480 | pemsley | 2008-10-08 13:57:00 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/greg-tests/07-ncs.scm Add NCS residue range edit test. ------------------------------------------------------------------------ r1479 | pemsley | 2008-10-08 13:16:37 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes updat dnotes. ------------------------------------------------------------------------ r1478 | pemsley | 2008-10-08 13:16:06 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES update release notes. ------------------------------------------------------------------------ r1477 | pemsley | 2008-10-08 11:47:26 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/build-it Resolve conflict in version number, python fixes. ------------------------------------------------------------------------ r1476 | b.lohkamp | 2008-10-08 09:14:19 +0100 (Wed, 08 Oct 2008) | 1 line Changed paths: M /trunk/src/gtk-manual.cc fixed Display Managers display style menu positions ------------------------------------------------------------------------ r1475 | pemsley | 2008-10-07 18:57:28 +0100 (Tue, 07 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Back to Python 2.5.1, that compiles on bragg3 (tests run). ------------------------------------------------------------------------ r1474 | pemsley | 2008-10-07 17:55:59 +0100 (Tue, 07 Oct 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/radacina_handcuffs-small.svg M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c Use GTK_RESPONSE_CANCEL in destroying a filechooser dialog (restraint_chooserdialog). Add an icons for restraints editor. ------------------------------------------------------------------------ r1473 | b.lohkamp | 2008-10-07 12:51:12 +0100 (Tue, 07 Oct 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/08_utils.py fixed import gobject for pygtk1 ------------------------------------------------------------------------ r1472 | pemsley | 2008-10-07 09:02:10 +0100 (Tue, 07 Oct 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Don't build gobject or pygtk if python is not given as an arg. ------------------------------------------------------------------------ r1471 | pemsley | 2008-10-07 08:48:20 +0100 (Tue, 07 Oct 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Don't build python if it is not passed as an arg. ------------------------------------------------------------------------ r1470 | pemsley | 2008-10-06 23:16:50 +0100 (Mon, 06 Oct 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc Return a value from the ghost operator<<. ------------------------------------------------------------------------ r1469 | pemsley | 2008-10-06 15:29:03 +0100 (Mon, 06 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Fix problem of missing NCS residue range operations for more than one peer chain. ------------------------------------------------------------------------ r1468 | pemsley | 2008-10-06 14:18:15 +0100 (Mon, 06 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Try again with build-web-page builder without pre-release source tar files. ------------------------------------------------------------------------ r1467 | pemsley | 2008-10-06 11:36:40 +0100 (Mon, 06 Oct 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Update web page builder to account for release time, where no pre-release source tar file exists. ------------------------------------------------------------------------ r1466 | b.lohkamp | 2008-10-05 18:05:58 +0100 (Sun, 05 Oct 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py add edit backbone torsion toolbutton ------------------------------------------------------------------------ r1465 | pemsley | 2008-10-05 12:00:15 +0100 (Sun, 05 Oct 2008) | 6 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh Remove usage of GTK_BROKEN. Add function atom_index_first_atom_in_residue_with_altconf(), used in show_rotamer_dialog. Now rotamer dialog can be bound to a key. Some debugging added to restraints-editor.hh to help fix the save restraints problem (referencing the wrong residue type). ------------------------------------------------------------------------ r1464 | pemsley | 2008-10-05 11:56:35 +0100 (Sun, 05 Oct 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Fix up writing of cif file (currently from restraints editor). ------------------------------------------------------------------------ r1463 | pemsley | 2008-10-05 11:47:36 +0100 (Sun, 05 Oct 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Comment out debugging for keybinding. ------------------------------------------------------------------------ r1462 | pemsley | 2008-10-01 07:13:54 +0100 (Wed, 01 Oct 2008) | 3 lines Changed paths: M /trunk/coords/mmdb.cc Cleanup with PDBCLEAN_ELEMENT after reading a coordintes file. (Generates elements where they were missing). ------------------------------------------------------------------------ r1461 | b.lohkamp | 2008-09-30 14:55:41 +0100 (Tue, 30 Sep 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/src/c-interface-preferences.cc fixed clash atoms, updated python extensions ------------------------------------------------------------------------ r1460 | b.lohkamp | 2008-09-30 10:26:58 +0100 (Tue, 30 Sep 2008) | 1 line Changed paths: M /trunk/build-it-win update windows autobuild script ------------------------------------------------------------------------ r1459 | pemsley | 2008-09-29 20:01:28 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Rework the Extensions menu reduce the length and sub-menu the items. ------------------------------------------------------------------------ r1458 | pemsley | 2008-09-29 17:53:01 +0100 (Mon, 29 Sep 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/dnotes M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/junk.cc Move to 0.5.1-pre-1 pre-release. Add a delete molecule button to display manager. Replace the display manager display and active toggle buttons with checkbuttons. ------------------------------------------------------------------------ r1457 | pemsley | 2008-09-29 17:45:11 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Bring back the missing flashing bond (was a typo, commented the wrong line). ------------------------------------------------------------------------ r1456 | pemsley | 2008-09-29 16:44:08 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: A /trunk/doc/tutorial-2.tex Add tutorial-2.tex ------------------------------------------------------------------------ r1455 | pemsley | 2008-09-29 16:41:40 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1454 | pemsley | 2008-09-26 17:19:46 +0100 (Fri, 26 Sep 2008) | 3 lines Changed paths: M /trunk/theor-helix-70.pdb Oops. move theor-helix to new pdb format. Bitten by my own dog-food... or something. ------------------------------------------------------------------------ r1453 | b.lohkamp | 2008-09-26 14:16:47 +0100 (Fri, 26 Sep 2008) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/08_utils.py proper test to import gobject ------------------------------------------------------------------------ r1452 | pemsley | 2008-09-25 17:12:34 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Handle typename in pygobject.h for CentOS4. ------------------------------------------------------------------------ r1451 | pemsley | 2008-09-25 16:33:31 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use the right file name for gobject. ------------------------------------------------------------------------ r1450 | pemsley | 2008-09-25 16:25:34 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use pygobject 2.4 if needed (e.g on CentOS 4). ------------------------------------------------------------------------ r1449 | pemsley | 2008-09-25 16:23:17 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py Add "import gobject" to tests. ------------------------------------------------------------------------ r1448 | pemsley | 2008-09-24 18:54:18 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: A /trunk/DONE M /trunk/TODO Update TODO, Put old TODOs in DONE. ------------------------------------------------------------------------ r1447 | pemsley | 2008-09-24 18:53:03 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/TODO Update todo list. ------------------------------------------------------------------------ r1446 | pemsley | 2008-09-24 14:14:25 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/build-it Tell us what the source tar file was when building coot. ------------------------------------------------------------------------ r1445 | pemsley | 2008-09-24 11:47:16 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Debug test for greg. ------------------------------------------------------------------------ r1444 | pemsley | 2008-09-24 09:10:52 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Fix formatting of relnotes. ------------------------------------------------------------------------ r1443 | pemsley | 2008-09-24 07:49:29 +0100 (Wed, 24 Sep 2008) | 6 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/pixmaps/add-alt-conf.svg A /trunk/pixmaps/coot-0.5.xpm M /trunk/scheme/coot-gui.scm M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Release 0.5 Change the splash screen Try to build a working version of pygobject on CentOS4 Name the release in the relnotes. Rework the add-alt-conf svg icon. ------------------------------------------------------------------------ r1442 | pemsley | 2008-09-23 14:36:21 +0100 (Tue, 23 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/get-ebi.scm Fix up the URL stub for the OCA server (Dirk Kostrewa). ------------------------------------------------------------------------ r1441 | pemsley | 2008-09-23 09:51:14 +0100 (Tue, 23 Sep 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Minor doc update. ------------------------------------------------------------------------ r1440 | pemsley | 2008-09-22 18:10:07 +0100 (Mon, 22 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1439 | pemsley | 2008-09-22 18:09:43 +0100 (Mon, 22 Sep 2008) | 2 lines Changed paths: M /trunk/density-contour/Makefile.am Tidy up a tiny problem noted by new automake. ------------------------------------------------------------------------ r1438 | pemsley | 2008-09-22 18:07:14 +0100 (Mon, 22 Sep 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1437 | b.lohkamp | 2008-09-22 16:50:28 +0100 (Mon, 22 Sep 2008) | 1 line Changed paths: M /trunk/python/coot_utils.py fix for keyboard mapping on some windows systems ------------------------------------------------------------------------ r1436 | b.lohkamp | 2008-09-22 16:44:15 +0100 (Mon, 22 Sep 2008) | 1 line Changed paths: M /trunk/src/c-interface-gui.cc fixed file chooser saved size ------------------------------------------------------------------------ r1435 | b.lohkamp | 2008-09-22 11:33:30 +0100 (Mon, 22 Sep 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/c-interface-gui.cc 'current directory' for filechooser ------------------------------------------------------------------------ r1434 | b.lohkamp | 2008-09-21 21:56:54 +0100 (Sun, 21 Sep 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/src/callbacks.c filechooser resize 'fix' ------------------------------------------------------------------------ r1433 | pemsley | 2008-09-21 12:15:52 +0100 (Sun, 21 Sep 2008) | 3 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh Use dictionary (where possible) to generate bonds (contacts) for atom tree generation when applying torsions in wiggly ligands. ------------------------------------------------------------------------ r1432 | pemsley | 2008-09-21 00:47:54 +0100 (Sun, 21 Sep 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.hh M /trunk/ligand/chi-angles.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc Fix up crash/failure of ligand search when period caused by torsion period of 0. Add set_debug_wiggly_ligands() function. ------------------------------------------------------------------------ r1431 | pemsley | 2008-09-20 11:22:05 +0100 (Sat, 20 Sep 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c Rework the #ifdefs on file chooser/selector functions. ------------------------------------------------------------------------ r1430 | pemsley | 2008-09-19 16:00:25 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/extensions.scm Enable python code from scheme - for side chain docking and running refmac. ------------------------------------------------------------------------ r1429 | pemsley | 2008-09-19 15:46:39 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-navigation-gtk2.cc Also, similarly protect the _row_actived() function. ------------------------------------------------------------------------ r1428 | pemsley | 2008-09-19 15:44:45 +0100 (Fri, 19 Sep 2008) | 3 lines Changed paths: M /trunk/src/graphics-info-navigation-gtk2.cc Add null pointer protection (from intelligent_this_residue_mmdb_atom()) in residue_tree_residue_row_activated(). ------------------------------------------------------------------------ r1427 | pemsley | 2008-09-19 15:11:28 +0100 (Fri, 19 Sep 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/src/coot_pythonmodule.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Remove debugging of erase_last_molecule(). Remove (make invisible) skeleton prune and colour from the GUI. ------------------------------------------------------------------------ r1426 | pemsley | 2008-09-19 13:46:18 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Remove debugging from python (pygtk) macro. ------------------------------------------------------------------------ r1425 | pemsley | 2008-09-19 12:32:10 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi More on NCS ghosts. ------------------------------------------------------------------------ r1424 | pemsley | 2008-09-19 12:31:09 +0100 (Fri, 19 Sep 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Now GSL is 1.11 we need an exact test for the version number because 1.11 is numerically less than 1.3. ------------------------------------------------------------------------ r1423 | b.lohkamp | 2008-09-19 11:25:40 +0100 (Fri, 19 Sep 2008) | 1 line Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc fixes for model_toolbar ------------------------------------------------------------------------ r1422 | pemsley | 2008-09-18 18:09:39 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove references to glitz, cairo, fontconfig. ------------------------------------------------------------------------ r1421 | pemsley | 2008-09-18 17:00:48 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Add forgotten generic-display-object.hh. ------------------------------------------------------------------------ r1420 | b.lohkamp | 2008-09-18 15:47:30 +0100 (Thu, 18 Sep 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c model_toolbar can dock top and bottom, and has a pop-up menu added model_toolbar function to reattach the toolbar removed handle_read_draw_probe_dots_unformatted_py and reworked handle_read_draw_probe_dots_unformatted to prefer either python or scheme gui ------------------------------------------------------------------------ r1419 | pemsley | 2008-09-18 14:53:51 +0100 (Thu, 18 Sep 2008) | 3 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/globjects.cc Add hybrid_36-reading scan line to probe_dots_unformatted. Needs to be configurable perhaps. ------------------------------------------------------------------------ r1418 | pemsley | 2008-09-18 14:45:11 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1417 | pemsley | 2008-09-18 14:44:21 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/gdk-keysyms.cc Add some comments. ------------------------------------------------------------------------ r1416 | pemsley | 2008-09-18 14:41:54 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Remove telling us that a key was pressed. ------------------------------------------------------------------------ r1415 | pemsley | 2008-09-18 13:01:08 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-render.cc Fix number format output problem for generic dots. ------------------------------------------------------------------------ r1414 | pemsley | 2008-09-17 18:02:01 +0100 (Wed, 17 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/happy-coot-diary.html M /trunk/src/coot-render.hh A /trunk/src/generic-display-object.hh M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h Add the ability to render (raster3d) generic display objects. ------------------------------------------------------------------------ r1413 | b.lohkamp | 2008-09-17 14:59:59 +0100 (Wed, 17 Sep 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows build script ------------------------------------------------------------------------ r1412 | pemsley | 2008-09-16 17:09:47 +0100 (Tue, 16 Sep 2008) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 change the version of mmdb that we need. ------------------------------------------------------------------------ r1411 | pemsley | 2008-09-16 13:51:33 +0100 (Tue, 16 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/gdk-keysyms.cc Correct () to [] in key binding codes. ------------------------------------------------------------------------ r1410 | b.lohkamp | 2008-09-16 11:15:22 +0100 (Tue, 16 Sep 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/python/get_ebi.py M /trunk/python/mutate.py M /trunk/python/refmac.py M /trunk/python/shelx.py M /trunk/python-tests/08_utils.py M /trunk/src/graphics-info.h fix rama-data for windows ------------------------------------------------------------------------ r1409 | pemsley | 2008-09-15 13:40:32 +0100 (Mon, 15 Sep 2008) | 2 lines Changed paths: M /trunk/cootrc Fix syntax of small_font, now consistent with others. ------------------------------------------------------------------------ r1408 | pemsley | 2008-09-15 10:27:34 +0100 (Mon, 15 Sep 2008) | 2 lines Changed paths: M /trunk/src/c-interface-superpose.cc Remove some debugging. ------------------------------------------------------------------------ r1407 | pemsley | 2008-09-15 10:26:21 +0100 (Mon, 15 Sep 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Mark the fc5 python build as python. ------------------------------------------------------------------------ r1406 | b.lohkamp | 2008-09-14 15:18:05 +0100 (Sun, 14 Sep 2008) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade A /trunk/pixmaps/map.svg M /trunk/python/a_rapper_gui.py M /trunk/python/background_demo.py M /trunk/python/bones_reader.py M /trunk/python/brute_lsqman.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/filter.py M /trunk/python/fitting.py M /trunk/python/gap.py M /trunk/python/generic_objects.py M /trunk/python/get_ebi.py M /trunk/python/group_settings.py M /trunk/python/hello.py M /trunk/python/libcheck.py M /trunk/python/mutate.py M /trunk/python/ncs.py M /trunk/python/povray.py M /trunk/python/python_coot_docs.py M /trunk/python/raster3d.py M /trunk/python/refmac.py M /trunk/python/shelx.py M /trunk/python/shelx_extensions.py M /trunk/python/tips_gui.py M /trunk/python/unittest_extensions.py M /trunk/python/what_check.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/04_cootaneer.py M /trunk/python-tests/05_rna_ghosts.py M /trunk/python-tests/06_ssm.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/begin.py M /trunk/python-tests/coot_unittest.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh updated python(-test) scripts to GPL 3 proper keyboard mapping for keybinding in pygtk 'proper' map icon for preferences ------------------------------------------------------------------------ r1405 | pemsley | 2008-09-14 12:35:00 +0100 (Sun, 14 Sep 2008) | 5 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/junk.cc M /trunk/src/support.c M /trunk/src/support.h Change the Undo molecule chooser to the in-build one. Set the active undo molecule correctly. Update the interface files Move refmac button press handler into c-interface-gui.cc ------------------------------------------------------------------------ r1404 | pemsley | 2008-09-14 11:05:17 +0100 (Sun, 14 Sep 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.c M /trunk/src/support.h Change the label on the Search Monomer Library dialog. Update splash screens on gtk1 version. ------------------------------------------------------------------------ r1403 | pemsley | 2008-09-13 19:30:01 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/greg-tests/08-utils.scm M /trunk/scheme/get-ebi.scm M /trunk/src/molecule-class-info-other.cc Remove debugging apparent in the test logs. ------------------------------------------------------------------------ r1402 | pemsley | 2008-09-13 18:53:05 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/ligand/ligand-extras.cc Fix short int (0) to std::string ambiguity. Fixes Bernhard's crash. ------------------------------------------------------------------------ r1401 | pemsley | 2008-09-13 18:13:31 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix typo in previous debugging comment removal. ------------------------------------------------------------------------ r1400 | pemsley | 2008-09-13 15:57:24 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Remove cispep debugging. ------------------------------------------------------------------------ r1399 | pemsley | 2008-09-13 14:13:07 +0100 (Sat, 13 Sep 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Check that chain pointer is valid before using it in cis_peptides_info_from_coords(). Fixes baton build crash. ------------------------------------------------------------------------ r1398 | pemsley | 2008-09-11 09:00:36 +0100 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/ligand/ligand-extras.cc M /trunk/ligand/test-fffear-in-coot.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh when in flood mode, make the output residue name and atom name be DUM. ------------------------------------------------------------------------ r1397 | pemsley | 2008-09-11 07:44:17 +0100 (Thu, 11 Sep 2008) | 2 lines Changed paths: D /trunk/pixmaps/arashiyama-park-bevelled.jpg D /trunk/pixmaps/arashiyama-park.xcf D /trunk/pixmaps/coot-0.2.xpm D /trunk/pixmaps/coot-0.3.xpm D /trunk/pixmaps/coot-0.4-alternate.xpm D /trunk/pixmaps/coot-0.4-pre.xpm D /trunk/pixmaps/coot-0.4.xpm D /trunk/pixmaps/coot-16-bevel.xpm Remove unneeded xpm pixmaps and other images to make the tar ball smaller. ------------------------------------------------------------------------ r1396 | pemsley | 2008-09-11 07:15:34 +0100 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Chnage the source of gtkglext to software/extras. ------------------------------------------------------------------------ r1395 | pemsley | 2008-09-10 22:14:40 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: A /trunk/coot-utils/xmap-stats.cc A /trunk/coot-utils/xmap-stats.hh Add forgotten xmap-stats files. ------------------------------------------------------------------------ r1394 | pemsley | 2008-09-10 19:40:07 +0100 (Wed, 10 Sep 2008) | 3 lines Changed paths: M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc Adjust the output filenames, use water_molecule, to be writen out to the file name given to findwaters. ------------------------------------------------------------------------ r1393 | pemsley | 2008-09-10 19:25:35 +0100 (Wed, 10 Sep 2008) | 4 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/dnotes M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/xmap-utils.cc M /trunk/src/xmap-utils.h Improve the flooding mechanism. Not too hard, as it turns out, use peaksearch, not clusters and move the xmap-utils (mean_and_variance) into coot-utils, from src dir. ------------------------------------------------------------------------ r1392 | pemsley | 2008-09-10 15:51:19 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1391 | pemsley | 2008-09-10 13:23:45 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface.cc Fix problem of recentering when there are no coordinates molecules displayed. ------------------------------------------------------------------------ r1390 | pemsley | 2008-09-10 13:09:57 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/ligand/find-waters.cc Add a check that the mtz file is properly read before using the map. ------------------------------------------------------------------------ r1389 | pemsley | 2008-09-10 10:05:16 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/ligand/ligand-extras.cc Remove debugging output for flood mode. ------------------------------------------------------------------------ r1388 | pemsley | 2008-09-10 10:04:01 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/configure.in Remove HAVE_SYS_STDTYPES_H debugging from configure. ------------------------------------------------------------------------ r1387 | pemsley | 2008-09-10 09:58:56 +0100 (Wed, 10 Sep 2008) | 3 lines Changed paths: M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc Tidy up find waters output - leave it for there now. I think findwaters needs a new algorithm in flood mode. Now is not the time. ------------------------------------------------------------------------ r1386 | pemsley | 2008-09-10 09:50:43 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh Improvements to find-waters --flood mode. ------------------------------------------------------------------------ r1385 | pemsley | 2008-09-10 08:25:16 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r1384 | pemsley | 2008-09-10 08:21:32 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/autogen.sh A bit of feedback when using Darwin. ------------------------------------------------------------------------ r1383 | pemsley | 2008-09-10 08:20:36 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/cootaneer/Makefile.am Don't install cootaneer_demo. ------------------------------------------------------------------------ r1382 | pemsley | 2008-09-09 19:28:45 +0100 (Tue, 09 Sep 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c Correctly type the new togglebutton when looking up the dialog. ------------------------------------------------------------------------ r1381 | pemsley | 2008-09-09 19:24:45 +0100 (Tue, 09 Sep 2008) | 6 lines Changed paths: M /trunk/README M /trunk/RELEASE-NOTES M /trunk/autogen.sh M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Refactor the chi angles dialog filling, add a check button to add hydrogen torsions/chi angles. Add a c-interface function used by the check button callback, the dialog need to know its own residue type. clear_out_container() utility function added. ------------------------------------------------------------------------ r1380 | b.lohkamp | 2008-09-09 15:50:25 +0100 (Tue, 09 Sep 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/python/libcheck.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/03_ligand.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c updated python tests refine-toolbar show/hide & left/right in preferences ------------------------------------------------------------------------ r1379 | b.lohkamp | 2008-09-09 07:55:10 +0100 (Tue, 09 Sep 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/c-interface.cc M /trunk/src/command-line.cc fixed test fail on python keybinding ------------------------------------------------------------------------ r1378 | b.lohkamp | 2008-09-08 20:41:39 +0100 (Mon, 08 Sep 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/libcheck.py M /trunk/src/command-line.cc M /trunk/src/main.cc stepped rama refine for python key bindings for python small-screen command line option (replaces eee) fix gdb crash on windows on loading icons ------------------------------------------------------------------------ r1377 | pemsley | 2008-09-08 14:20:24 +0100 (Mon, 08 Sep 2008) | 4 lines Changed paths: M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/geometry/Makefile.am M /trunk/ligand/ligand.cc M /trunk/mapview.glade M /trunk/scheme/coot-gui.scm M /trunk/src/Makefile.am M /trunk/src/graphics-info-defines.cc M /trunk/src/interface.c Add a setting of HAVE_SYS_TYPES_H, needed for loading a guile header. Fix button label for Ramachandran Restraints in Gtk1 version (TS). Update notes. ------------------------------------------------------------------------ r1376 | pemsley | 2008-09-07 18:35:34 +0100 (Sun, 07 Sep 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Use $PYTHON, not python to get python variables, for CFLAGS and linking. ------------------------------------------------------------------------ r1375 | pemsley | 2008-09-07 17:51:31 +0100 (Sun, 07 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add a definition for set-find-hydrogen-torsions for doc snarfing. ------------------------------------------------------------------------ r1374 | pemsley | 2008-09-01 15:41:01 +0100 (Mon, 01 Sep 2008) | 4 lines Changed paths: M /trunk/doc/tutorial.tex Update tutorial. Fixes from Kevin, except the use of png instead of ps for figures (bounding box problems). ps remain. More NCS text. ------------------------------------------------------------------------ r1373 | pemsley | 2008-08-31 15:35:49 +0100 (Sun, 31 Aug 2008) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/pixmaps/edit-chi.svg M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Changes from Osaka (and Tokyo a bit): Create function make_mols_from_atom_selection, which makes a selected and masked molecule for use in rigid body fitting. Add internal test for this. Refactor rigid body fitting, so that we can script it and pass an mmdb atom selection. This is a feature for Catherine Lawson. Remove some casting from mmdb char * args (now const). ------------------------------------------------------------------------ r1372 | pemsley | 2008-08-26 16:57:22 +0100 (Tue, 26 Aug 2008) | 2 lines Changed paths: M /trunk/cootaneer/cootaneer-demo.cpp uncast the call to ReadPDBASCII now that we are using the new mmdb. ------------------------------------------------------------------------ r1371 | pemsley | 2008-08-23 13:50:28 +0100 (Sat, 23 Aug 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add a test for mangling hydrogen names from a 3.0 file. Fails if Coot not linked with mmdb-1.12 or better. ------------------------------------------------------------------------ r1370 | pemsley | 2008-08-22 18:26:42 +0100 (Fri, 22 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add some documentation for mutate-by-overlap. ------------------------------------------------------------------------ r1369 | b.lohkamp | 2008-08-21 17:51:57 +0100 (Thu, 21 Aug 2008) | 1 line Changed paths: M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/globjects.cc M /trunk/src/main.cc eee command line option for small screens ------------------------------------------------------------------------ r1368 | b.lohkamp | 2008-08-20 19:51:52 +0100 (Wed, 20 Aug 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/what_check.py what_check.py functional ------------------------------------------------------------------------ r1367 | pemsley | 2008-08-20 17:26:21 +0100 (Wed, 20 Aug 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes ------------------------------------------------------------------------ r1366 | pemsley | 2008-08-20 17:24:18 +0100 (Wed, 20 Aug 2008) | 2 lines Changed paths: M /trunk/src/pick.cc M /trunk/src/pick.h Add some more debugging for atom picking. ------------------------------------------------------------------------ r1365 | b.lohkamp | 2008-08-20 11:18:54 +0100 (Wed, 20 Aug 2008) | 1 line Changed paths: M /trunk/python/a_rapper_gui.py A /trunk/python/what_check.py updated python rapper gui, added what_check.py (both need testing) ------------------------------------------------------------------------ r1364 | pemsley | 2008-08-19 14:49:42 +0100 (Tue, 19 Aug 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add forgotten get-refmac-sad-atom-info-scm for doc snarfing. ------------------------------------------------------------------------ r1363 | b.lohkamp | 2008-08-19 14:08:22 +0100 (Tue, 19 Aug 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/coot-gtk2.glade M /trunk/cootrc M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc mmdb 1.12 for windows build scheme refmac for SAD, TWIN, NCS, TLS, rigid body etc. all toolbar (and button) icons are set to 16x16 model/fit/refine dialog has svgs instead of pngs ------------------------------------------------------------------------ r1362 | pemsley | 2008-08-18 17:04:42 +0100 (Mon, 18 Aug 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm M /trunk/dnotes Use mmdb version 1.12 Put link to source build log and dir of program builds in binary cells. ------------------------------------------------------------------------ r1361 | pemsley | 2008-08-18 14:07:53 +0100 (Mon, 18 Aug 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Put the build dir into the links. ------------------------------------------------------------------------ r1360 | pemsley | 2008-08-17 20:13:19 +0100 (Sun, 17 Aug 2008) | 4 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm Fix syntax error in coot-has-pygtk?. Add Extensions menu item to refine a protein with Rama restraints. Re-works stepped-refine to allow the use of Ramachandran restraints. ------------------------------------------------------------------------ r1359 | pemsley | 2008-08-17 00:48:51 +0100 (Sun, 17 Aug 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/scheme/libcheck.scm M /trunk/src/restraints-editor.cc Add some -b-D extras to libcheck interface - doesn't seem to work though. In the restraints editor, if the tlc is missing, make the tlc be a copy of the comp_id. ------------------------------------------------------------------------ r1358 | pemsley | 2008-08-15 16:00:36 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Correct a few syntax errors in the user manual. ------------------------------------------------------------------------ r1357 | b.lohkamp | 2008-08-15 14:38:54 +0100 (Fri, 15 Aug 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/cmtz-interface.cc M /trunk/src/graphics-info.cc fixes for refmac SAD refinement connected most new refmac function in guile ------------------------------------------------------------------------ r1356 | pemsley | 2008-08-15 13:20:04 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/coords/mmdb.cc Ooops - remove the debugging code (commented out fix_wrapped_names()). ------------------------------------------------------------------------ r1355 | pemsley | 2008-08-15 11:53:51 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/dnotes M /trunk/happy-coot-diary.html Add a if (0) round the atom name debugging. I could be coming back to it. ------------------------------------------------------------------------ r1354 | pemsley | 2008-08-15 11:52:51 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi document --code for accession codes. ------------------------------------------------------------------------ r1353 | pemsley | 2008-08-15 11:49:37 +0100 (Fri, 15 Aug 2008) | 5 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/add-c-extern.sh M /trunk/src/c-interface.cc M /trunk/src/command-line.cc D /trunk/src/command-line.h A /trunk/src/command-line.hh (from /trunk/src/command-line.h:1351) M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/interface.h M /trunk/src/main.cc M /trunk/src/support.h Add the reading of accesion code files from the command line (slow). add-c-extern.sh condition now GTK_MAJOR_VERSION > 1, not dependent on the GTK_MINOR_VERSION. Works better for CentOS build. commanand-line.h renamed to command-line.hh. ------------------------------------------------------------------------ r1352 | pemsley | 2008-08-15 11:30:16 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/build-it Fix test info syntax error. ------------------------------------------------------------------------ r1351 | pemsley | 2008-08-14 16:18:28 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1350 | pemsley | 2008-08-14 16:00:52 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/graphics-info.cc M /trunk/src/interface.c M /trunk/src/interface.h Add chi squared values for gtk1 accept/reject dialog. ------------------------------------------------------------------------ r1349 | b.lohkamp | 2008-08-14 14:58:01 +0100 (Thu, 14 Aug 2008) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/povray.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/refmac.scm coot-has-pygtk? for scheme: run cootaneering and read_refmac_log if we have pygtk povray name change for 64bit windows ------------------------------------------------------------------------ r1348 | pemsley | 2008-08-14 14:27:47 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Remove debugging from resdiue editor creator. ------------------------------------------------------------------------ r1347 | pemsley | 2008-08-14 14:22:57 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Some debugging on the residue editor creator. ------------------------------------------------------------------------ r1346 | pemsley | 2008-08-14 13:36:26 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c Support code for restraints editor without gtk_combo_box_get_active_text(). ------------------------------------------------------------------------ r1345 | b.lohkamp | 2008-08-14 12:42:32 +0100 (Thu, 14 Aug 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/pixmaps/phenixed.svg M /trunk/pixmaps/residue-info.svg M /trunk/pixmaps/sequence-view.svg M /trunk/python/gap.py M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h add terminal residue mutates if associated sequence (no autofit!?) more changes to pixmap svg fonts ------------------------------------------------------------------------ r1344 | pemsley | 2008-08-14 11:29:41 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi update docs (command line args). ------------------------------------------------------------------------ r1343 | pemsley | 2008-08-14 11:12:13 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/command-line.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Enable -c direct commands from the command line. ------------------------------------------------------------------------ r1342 | pemsley | 2008-08-14 10:37:28 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/command-line.cc M /trunk/src/command-line.h partly enable executable commands from the command line. ------------------------------------------------------------------------ r1341 | pemsley | 2008-08-14 09:49:52 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/pick.cc Add displayed info into atom picking debug info. ------------------------------------------------------------------------ r1340 | pemsley | 2008-08-14 09:23:06 +0100 (Thu, 14 Aug 2008) | 8 lines Changed paths: M /trunk/autogen.sh M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/pick.cc Add code to output number of links (will use them for bonding/refinement later). Fix NCS chain documentation. A bit better build output when not running tests. Add a debug_atom_picking setting. Remove char * casting from a graphics-info-navigation.cc atom selection function. ------------------------------------------------------------------------ r1339 | b.lohkamp | 2008-08-13 11:26:53 +0100 (Wed, 13 Aug 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/gap.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h gap/loop fitting will fit both directions and fire up a GUI to select (python) fix for no-graphics ------------------------------------------------------------------------ r1338 | pemsley | 2008-08-12 14:52:48 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py Update cis peptide python test. ------------------------------------------------------------------------ r1337 | pemsley | 2008-08-12 13:59:39 +0100 (Tue, 12 Aug 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Cispep test is now expected to pass (note that an unexpected pass causes an overall fail - and the tar file is not built). ------------------------------------------------------------------------ r1336 | pemsley | 2008-08-12 12:14:50 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/src/align.cc Tweak the arg to Get1LetterCode(rn, r). Not sure how this works... ------------------------------------------------------------------------ r1335 | b.lohkamp | 2008-08-12 12:13:59 +0100 (Tue, 12 Aug 2008) | 4 lines Changed paths: A /trunk/bldnotes M /trunk/build-it-win M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-utils.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc added EDS references notebook tab Windows adjustments for icon size change on small screens added bldnotes ------------------------------------------------------------------------ r1334 | pemsley | 2008-08-12 07:30:50 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 Fix up the mmdb test so that is it consistemt with the code (using cpstr). ------------------------------------------------------------------------ r1333 | pemsley | 2008-08-12 01:20:23 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/build-it Use mmdb version 1.11. ------------------------------------------------------------------------ r1332 | pemsley | 2008-08-11 20:59:25 +0100 (Mon, 11 Aug 2008) | 5 lines Changed paths: M /trunk/autogen.sh M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/db-main/db-strands.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/high-res/globularize.cc M /trunk/high-res/trace-high-res.cc M /trunk/ideal/pepflip.cc M /trunk/ideal/with-map.cc M /trunk/ligand/find-ligand.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/test-fffear-in-coot.cc M /trunk/ligand/test-helix-placement.cc M /trunk/sequence-view/sequence-view.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/command-line.cc M /trunk/src/density-score-by-residue.cc M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/post-process-coot-wrap-guile.sh A /trunk/src/post-process-coot-wrap-python.sh M /trunk/surface/CXXFortranFile.cpp M /trunk/surface/CXXFortranFile.h Changes for mmdb 1.11 and GCC 4.3 Clean up char * vs const char * usage. More diagnostics in ligand tests. Tweak the post-processing of the guile wrap files for char * -> const char *. ------------------------------------------------------------------------ r1331 | pemsley | 2008-08-11 19:47:49 +0100 (Mon, 11 Aug 2008) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 Add in test for CISPEP support to mmdb. ------------------------------------------------------------------------ r1330 | b.lohkamp | 2008-08-11 15:30:58 +0100 (Mon, 11 Aug 2008) | 4 lines Changed paths: M /trunk/python/extensions.py M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/post-gtk2-glade.sh ncs submenu in python extensions antialiased gtk+-2.0 icons refinement toolbar icons shrink automatically on small screens ------------------------------------------------------------------------ r1329 | pemsley | 2008-08-11 13:30:55 +0100 (Mon, 11 Aug 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Properly set the scroll wheel map in the state file. Add documentation for moving zero occupancy atoms. Add an option not to move atoms with zero occupancy in refinement. ------------------------------------------------------------------------ r1328 | pemsley | 2008-08-11 09:34:40 +0100 (Mon, 11 Aug 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/doc/user-manual.texi M /trunk/src/c-inner-main.c Update documentation (NCS chain). ------------------------------------------------------------------------ r1327 | pemsley | 2008-08-11 01:00:20 +0100 (Mon, 11 Aug 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a GUI for NCS chain. ------------------------------------------------------------------------ r1326 | pemsley | 2008-08-09 06:44:42 +0100 (Sat, 09 Aug 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm We need a GUI to associate the sequence, even if python is available. ------------------------------------------------------------------------ r1325 | b.lohkamp | 2008-08-08 14:20:14 +0100 (Fri, 08 Aug 2008) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/gap.py M /trunk/python/mutate.py M /trunk/python/shelx_extensions.py M /trunk/scheme/gap.scm file selector/chooser switch in python scripts toolbuttons can have a suggested icon fit loop works backwards for python AND scheme now ------------------------------------------------------------------------ r1324 | b.lohkamp | 2008-08-07 17:01:50 +0100 (Thu, 07 Aug 2008) | 6 lines Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/azerbaijan.svg A /trunk/pixmaps/azerbaijan2.svg M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/extensions.py M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c fixed refmac dialog (gtk2, python) hide/show for docked accept/reject refinement toolbar (incl. preferences) associate sequence in py extensions py extension have accelerator added garib pixmaps... ------------------------------------------------------------------------ r1323 | pemsley | 2008-08-05 04:19:09 +0100 (Tue, 05 Aug 2008) | 3 lines Changed paths: M /trunk/src/graphics-info.cc Make the traffic light distortion for Rama follow the scale of restraints geometry distortion. ------------------------------------------------------------------------ r1322 | pemsley | 2008-08-05 04:09:35 +0100 (Tue, 05 Aug 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Tweak the scale of the Ramachandran plot distortion. ------------------------------------------------------------------------ r1321 | pemsley | 2008-08-05 04:08:30 +0100 (Tue, 05 Aug 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/happy-coot-diary.html M /trunk/ideal/simple-restraint.cc M /trunk/mapview.glade M /trunk/src/graphics-info.cc M /trunk/src/interface.h Some forgotten things on Rama updates? (Don't know how they got lost). ------------------------------------------------------------------------ r1320 | b.lohkamp | 2008-08-03 12:42:20 +0100 (Sun, 03 Aug 2008) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cmtz-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc refmac twin option implemented ------------------------------------------------------------------------ r1319 | pemsley | 2008-08-01 17:52:00 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1318 | pemsley | 2008-08-01 17:00:13 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Tweak the colour scheme for Ramachandran geometry box. ------------------------------------------------------------------------ r1317 | pemsley | 2008-08-01 16:24:32 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h M /trunk/src/testing.cc Add GUI check button for Ramachandran restraints. ------------------------------------------------------------------------ r1316 | pemsley | 2008-08-01 15:25:31 +0100 (Fri, 01 Aug 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc Fix up the setting of fixed atom in the Ramachandran restraints. By Jove, I think it's working now! ------------------------------------------------------------------------ r1315 | pemsley | 2008-08-01 13:19:37 +0100 (Fri, 01 Aug 2008) | 3 lines Changed paths: M /trunk/pixmaps/change-chain-id.svg Make a test update of change-chain-id.svg with Inkscape. test font testings are preserved. ------------------------------------------------------------------------ r1314 | pemsley | 2008-08-01 13:10:41 +0100 (Fri, 01 Aug 2008) | 3 lines Changed paths: M /trunk/greg-tests/08-utils.scm M /trunk/src/c-interface.cc Add test python command for unknown python command. Fix up safe_python_command_with_return to handle unknown python command. ------------------------------------------------------------------------ r1313 | pemsley | 2008-08-01 10:58:19 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/src/fix-filechooser-sentinels.awk M /trunk/src/gtk2-interface.c Also fix sentinels of new (refmac) file choosers. ------------------------------------------------------------------------ r1312 | pemsley | 2008-08-01 10:33:27 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: A /trunk/src/fix-filechooser-sentinels.awk M /trunk/src/fixup-gtk2-interface.sh M /trunk/src/gtk2-interface.c Add script to fix sentinels in file_chooser_dialog_new. ------------------------------------------------------------------------ r1311 | b.lohkamp | 2008-08-01 08:36:52 +0100 (Fri, 01 Aug 2008) | 1 line Changed paths: M /trunk/pixmaps/change-chain-id.svg M /trunk/pixmaps/chiral.svg M /trunk/pixmaps/connect-to-usf.svg M /trunk/pixmaps/density-fit.svg M /trunk/pixmaps/edit-chi.svg M /trunk/pixmaps/geom.svg M /trunk/pixmaps/gln-asn-b-factors.svg M /trunk/pixmaps/gln-asn-b-factorssvg.svg M /trunk/pixmaps/renumber-residues.svg M /trunk/pixmaps/side-chain-180.svg font lists for svgs with text ------------------------------------------------------------------------ r1310 | pemsley | 2008-07-31 12:39:29 +0100 (Thu, 31 Jul 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc Add in correct scale factor for phi and psi torsion gradients. Factor out multiplications in torsion gradients. ------------------------------------------------------------------------ r1309 | pemsley | 2008-07-31 12:01:27 +0100 (Thu, 31 Jul 2008) | 3 lines Changed paths: M /trunk/src/testing.cc Apply dx the other direction to get a better estimate of the numerical gradient. kdc_torsion_test() passes now. ------------------------------------------------------------------------ r1308 | pemsley | 2008-07-31 11:54:48 +0100 (Thu, 31 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Clean up kdc_torsion_test(). ------------------------------------------------------------------------ r1307 | pemsley | 2008-07-31 11:46:46 +0100 (Thu, 31 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Add in scale factor to convert dD/dx1 to dtheta/dx1 in kdc_torsion_test(). ------------------------------------------------------------------------ r1306 | b.lohkamp | 2008-07-31 08:16:22 +0100 (Thu, 31 Jul 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c atom_spec fix, some refmac additions & fixes ------------------------------------------------------------------------ r1305 | pemsley | 2008-07-31 00:22:26 +0100 (Thu, 31 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add Diagnosis for applying guile-gtk patch. ------------------------------------------------------------------------ r1304 | pemsley | 2008-07-30 18:57:26 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix typo in temp factor for *atom_info_string_py. ------------------------------------------------------------------------ r1303 | pemsley | 2008-07-30 18:22:13 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Updates relnotes. ------------------------------------------------------------------------ r1302 | pemsley | 2008-07-30 18:21:02 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix long-standing crash on opening cell and symmetry with no molecules read. ------------------------------------------------------------------------ r1301 | pemsley | 2008-07-30 17:53:36 +0100 (Wed, 30 Jul 2008) | 5 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc Change atom-info-string to return a SCM and atom_info_string_py to return a PyObject *. Add function to strip spaces from a string. Add some debugging to retraints editor startup (from callback.c) code. ------------------------------------------------------------------------ r1300 | b.lohkamp | 2008-07-30 15:57:18 +0100 (Wed, 30 Jul 2008) | 1 line Changed paths: M /trunk/python/clear_backup.py M /trunk/python/coot_gui.py M /trunk/src/molecule-class-info-maps.cc windows and python script fixes ------------------------------------------------------------------------ r1299 | pemsley | 2008-07-30 15:31:41 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/happy-coot-diary.html Test for gtk minor version, use that to apply guile-gtk patches. ------------------------------------------------------------------------ r1298 | pemsley | 2008-07-30 13:39:01 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use old version of pyobject if pkg-config is not new enough. ------------------------------------------------------------------------ r1297 | pemsley | 2008-07-30 12:34:27 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c GtkMenuToolButton does not exist for GTK 2.4. #ifdef it out. ------------------------------------------------------------------------ r1296 | pemsley | 2008-07-30 12:10:51 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjust test for up to date python. ------------------------------------------------------------------------ r1295 | pemsley | 2008-07-30 10:24:45 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c More fiddling with ifdefs to try to compile on Gtk 2.4 ------------------------------------------------------------------------ r1294 | pemsley | 2008-07-30 01:13:55 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/happy-coot-diary.html M /trunk/ifdef-for-create-aboutdialog.awk M /trunk/src/add-c-extern.sh M /trunk/src/fixup-gtk2-interface.sh M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Hand apply the edits to comment out the aboutdialog function when needed. ------------------------------------------------------------------------ r1293 | pemsley | 2008-07-30 00:38:30 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: A /trunk/ifdef-for-create-aboutdialog.awk Add awk to to #ifdef out the create_aboutdialog() function. ------------------------------------------------------------------------ r1292 | pemsley | 2008-07-29 22:10:52 +0100 (Tue, 29 Jul 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/doc/reference.tex M /trunk/happy-coot-diary.html M /trunk/high-res/sequence-assignment.cc M /trunk/src/callbacks.c M /trunk/src/testing.cc M /trunk/src/testing.hh Add in Kevin's torsion derivatives test. Some possible fixes for using Gtk version 2.4. ------------------------------------------------------------------------ r1291 | pemsley | 2008-07-29 22:03:24 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjust test for build_guile_gtk. ------------------------------------------------------------------------ r1290 | pemsley | 2008-07-29 21:41:07 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Correctly test the up to date python version. ------------------------------------------------------------------------ r1289 | pemsley | 2008-07-29 20:03:31 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1288 | pemsley | 2008-07-29 19:17:49 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add centos build info to web build status page. ------------------------------------------------------------------------ r1287 | b.lohkamp | 2008-07-29 12:03:42 +0100 (Tue, 29 Jul 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py update python scripting and python tests added "add alt conf" to coot_toolbuttons ------------------------------------------------------------------------ r1286 | pemsley | 2008-07-28 15:34:39 +0100 (Mon, 28 Jul 2008) | 9 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/geometry/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/happy-coot-diary.html M /trunk/ideal/Makefile.am M /trunk/macros/gtk-canvas.m4 M /trunk/scheme/coot-gui.scm A /trunk/scheme/what-check.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-validate.cc M /trunk/src/cmtz-interface.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Changes from Nijmegen. Add what-check check.db parser what-check.scm Added dict_link_chiral_t to dictionary. Added chem_link to dictionary. Add data_mods to dictionary - stub/code in progress. Fixed geometry's Makefile so that parallel make works. Update key bindings in the User Manual. Updates to compile without GTK_CANVAS. ------------------------------------------------------------------------ r1285 | pemsley | 2008-07-28 13:11:57 +0100 (Mon, 28 Jul 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-widget-work.cc M /trunk/src/molecule-class-info.h Updates to make side by side stereo work with display lists. We need first and second display lists when using side by side stereo. ------------------------------------------------------------------------ r1284 | pemsley | 2008-07-26 16:01:29 +0100 (Sat, 26 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1283 | pemsley | 2008-07-26 01:16:52 +0100 (Sat, 26 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1282 | pemsley | 2008-07-21 13:48:12 +0100 (Mon, 21 Jul 2008) | 2 lines Changed paths: A /trunk/ideal/logparse.awk Add logparse.awk ------------------------------------------------------------------------ r1281 | pemsley | 2008-07-21 10:23:34 +0100 (Mon, 21 Jul 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/tips-gui.scm M /trunk/src/c-interface-gui.cc Spell check user manual. Update notes. Remove debugging. ------------------------------------------------------------------------ r1280 | pemsley | 2008-07-19 00:19:35 +0100 (Sat, 19 Jul 2008) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/tips-gui.scm Remove bang directives, recommendation from Bill Scott (strange but true, it seems). Fiddle with the next release date. ------------------------------------------------------------------------ r1279 | pemsley | 2008-07-18 22:19:11 +0100 (Fri, 18 Jul 2008) | 6 lines Changed paths: M /trunk/coords/Cartesian.cc M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/surface/CXXQADSurface.cpp Enable Rama restraints colour box in refinement accept/reject dialog Return a GdkColor from a distortion, not a pointer. Scripting function set_numerical_gradients(int istate). Add a new release time for old-coot. Some small compilation clean-ups. ------------------------------------------------------------------------ r1278 | pemsley | 2008-07-18 02:16:24 +0100 (Fri, 18 Jul 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-rama.cc M /trunk/dnotes M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc update other files (committed from wrong directory). ------------------------------------------------------------------------ r1277 | pemsley | 2008-07-18 01:01:31 +0100 (Fri, 18 Jul 2008) | 8 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Tidy up the peptide torsion and rama refinement interface. fill_distortion_torsion_gradients() factored out and used in torsion restraints too. Flanking rama restraints added. However the Rama refinement still fails - no progress. Disappointing. But, if you don't turn on ramachandran refinement (not documented) , users can't the the failure. Needs more work (obviously). ------------------------------------------------------------------------ r1276 | pemsley | 2008-07-16 22:52:35 +0100 (Wed, 16 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1275 | pemsley | 2008-07-15 23:30:31 +0100 (Tue, 15 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1274 | pemsley | 2008-07-14 15:22:57 +0100 (Mon, 14 Jul 2008) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/ideal/lograma.cpp M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/testing.cc Remove debugging from lograma. Introduce my_df_torsions_internal - may be removed later. scale R the same in f and df. ------------------------------------------------------------------------ r1273 | pemsley | 2008-07-14 02:12:56 +0100 (Mon, 14 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/ligand.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h More tidying. More initialization of initialized variables. ------------------------------------------------------------------------ r1272 | pemsley | 2008-07-13 17:38:05 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.h Remove unneeded std::string in assignment of column labels in setup_internal(). ------------------------------------------------------------------------ r1271 | pemsley | 2008-07-13 16:29:38 +0100 (Sun, 13 Jul 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/db-main/db-main.cc M /trunk/geometry/protein-geometry.cc M /trunk/high-res/coot-atom-graph.cc M /trunk/high-res/sequence-assignment.cc M /trunk/ideal/Makefile.am M /trunk/ideal/lograma.cpp M /trunk/ideal/logramatest.cpp M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/ligand.hh M /trunk/mini-mol/mini-mol-utils.cc M /trunk/skeleton/BuildCas.cc M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Minor fixes, uninitialized variables etc found when using 4.3 with more checking options enabled. Some debugging added to simple-restraint.cc ------------------------------------------------------------------------ r1270 | pemsley | 2008-07-13 13:12:11 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Clean up the tests, more info on failures. ------------------------------------------------------------------------ r1269 | pemsley | 2008-07-13 12:35:54 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/cmtz-interface.cc M /trunk/src/gtk-manual.cc Some fixes for uninitalized variables. ------------------------------------------------------------------------ r1268 | pemsley | 2008-07-13 12:35:18 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/src/testing.cc Add some debugging for the setting of rama restraints. ------------------------------------------------------------------------ r1267 | pemsley | 2008-07-13 12:13:43 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add a function to hide and show the vertical modelling toolbar (its frame, really). ------------------------------------------------------------------------ r1266 | pemsley | 2008-07-12 16:23:45 +0100 (Sat, 12 Jul 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/testing.cc M /trunk/src/testing.hh More test code for Ramachandran refinement. ------------------------------------------------------------------------ r1265 | pemsley | 2008-07-12 16:23:01 +0100 (Sat, 12 Jul 2008) | 2 lines Changed paths: M /trunk/libtool autogen.sh hardy makes new libtool. ------------------------------------------------------------------------ r1264 | pemsley | 2008-07-12 10:54:08 +0100 (Sat, 12 Jul 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-rama.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/src/testing.cc Remove ramachandran_probability from coot-coord-utils. Update documentations. ------------------------------------------------------------------------ r1263 | pemsley | 2008-07-11 17:28:42 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi More formatting updates for the user manual. ------------------------------------------------------------------------ r1262 | pemsley | 2008-07-11 17:00:47 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/Makefile.am Add some info to doc Makfiles. ------------------------------------------------------------------------ r1261 | pemsley | 2008-07-11 16:50:57 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi More formatting updates for user manual. ------------------------------------------------------------------------ r1260 | pemsley | 2008-07-11 16:41:56 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Now the user manual compiles cleanly with texi2html 1.76. ------------------------------------------------------------------------ r1259 | pemsley | 2008-07-11 16:29:17 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi update user-manual. ------------------------------------------------------------------------ r1258 | pemsley | 2008-07-11 16:28:06 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: A /trunk/doc/coot-plain-2.jpg Add/update coot-plain-2.jpg for web version of manual. ------------------------------------------------------------------------ r1257 | pemsley | 2008-07-11 12:52:41 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: A /trunk/coot-utils/coot-rama.cc A /trunk/coot-utils/coot-rama.hh Add coot-rama files, where the moved phi/psi code now resides. ------------------------------------------------------------------------ r1256 | pemsley | 2008-07-11 12:51:55 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/AUTHORS M /trunk/TODO M /trunk/coot-utils/Makefile.am M /trunk/dnotes M /trunk/src/graphics-info.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh M /trunk/src/testing.cc Add internal test for ramachandran angles. Move phi_psi_t to utils. ------------------------------------------------------------------------ r1255 | pemsley | 2008-07-11 12:49:19 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add a macro for using active residue. ------------------------------------------------------------------------ r1254 | pemsley | 2008-07-11 00:45:38 +0100 (Fri, 11 Jul 2008) | 7 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-state.cc Rotate/translate and rotate around fragment centre works with the sliders. Ca Zone -> mainchain now pops up a dialog when then range is too short. set-matrix is saved to the status file. peptide plane restraints state is saved in state file if off. Plane restraints button in Refinement Control now behaves properly. Document the variable refmac-extra-params. ------------------------------------------------------------------------ r1253 | b.lohkamp | 2008-07-10 22:50:31 +0100 (Thu, 10 Jul 2008) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-build.cc M /trunk/src/callbacks.c M /trunk/src/cmtz-interface.cc more refmac gui functions (TWIN no working still) ------------------------------------------------------------------------ r1252 | pemsley | 2008-07-10 15:04:16 +0100 (Thu, 10 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add update_maps() function to the scripting layer. ------------------------------------------------------------------------ r1251 | pemsley | 2008-07-10 15:03:43 +0100 (Thu, 10 Jul 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes ------------------------------------------------------------------------ r1250 | b.lohkamp | 2008-07-10 13:57:37 +0100 (Thu, 10 Jul 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info.h updated refmac gui (gtk2) and made SAD functional (TWIN option needs some more testing) ------------------------------------------------------------------------ r1249 | pemsley | 2008-07-10 11:08:01 +0100 (Thu, 10 Jul 2008) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/testing.cc M /trunk/src/testing.hh Make atom_selection_container_t a class - at last. Use a vector of functions in testing. Add part of a test for ramachandran probabilities. ------------------------------------------------------------------------ r1248 | pemsley | 2008-07-09 18:53:00 +0100 (Wed, 09 Jul 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/testing.cc Add some testing features to install_simple_wiggly_ligands(). Throw an excetion now. ------------------------------------------------------------------------ r1247 | pemsley | 2008-07-09 14:36:20 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc A bit more tidying up in the monomer restraints scm code. ------------------------------------------------------------------------ r1246 | pemsley | 2008-07-09 13:48:00 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/tw/tw.cc Use SCM_CAR not scm_car and SCM_CDR nto scm_cdr, for 1.6 compatibility. ------------------------------------------------------------------------ r1245 | pemsley | 2008-07-09 12:31:33 +0100 (Wed, 09 Jul 2008) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-info.cc Add a stream output of a plane restraints. Correct addition of plane restraints from scm objects. Update test to test for correct plane restraint. ------------------------------------------------------------------------ r1244 | pemsley | 2008-07-09 08:52:29 +0100 (Wed, 09 Jul 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-info.cc Change monomer bond restraint test to use regularize, not refine. Adjustments in reading SCM restraints. ------------------------------------------------------------------------ r1243 | pemsley | 2008-07-09 01:57:03 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/begin.grg M /trunk/src/c-interface-info.cc Oops - revert previous change (set-monomer and test had not been likewise adjusted). ------------------------------------------------------------------------ r1242 | pemsley | 2008-07-09 01:26:38 +0100 (Wed, 09 Jul 2008) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-info.cc Remove the extra list encapsulting the key in the monomer-restraints alists. So now (assoc-ref restraints key) returns a simple list, not a list within a list. ------------------------------------------------------------------------ r1241 | pemsley | 2008-07-09 01:00:00 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes update dnotes an rel notes. ------------------------------------------------------------------------ r1240 | pemsley | 2008-07-08 21:37:12 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1239 | pemsley | 2008-07-08 18:30:57 +0100 (Tue, 08 Jul 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Add Coot News to About dialog. Make better names for new molecules from map-transformation using lsq gui. ------------------------------------------------------------------------ r1238 | pemsley | 2008-07-08 16:55:31 +0100 (Tue, 08 Jul 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/ligand/rotamer.hh M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-references.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Change the probability tables so that they are loaded when needed, not at startup. Add a reference tab for the Uppsala Electron Density Server. Note: This may mess badly with src/gtk2-interface.c, so some rebuilding of the interface source may be needed. ------------------------------------------------------------------------ r1237 | pemsley | 2008-07-08 16:52:55 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade Make a coot-gtk2.glade that works with glade-2.10.0. ------------------------------------------------------------------------ r1236 | pemsley | 2008-07-08 15:13:53 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1235 | pemsley | 2008-07-08 13:07:26 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Fix up coot-has-python-p for snarfing docs. ------------------------------------------------------------------------ r1234 | pemsley | 2008-07-08 13:03:13 +0100 (Tue, 08 Jul 2008) | 3 lines Changed paths: M /trunk/ligand/primitive-chi-angles.hh M /trunk/src/c-interface-info.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Fix chi angle problem on using residue info on a GLY or ALA. Some initial code for testing wiggly ligands. ------------------------------------------------------------------------ r1233 | b.lohkamp | 2008-07-08 08:17:15 +0100 (Tue, 08 Jul 2008) | 1 line Changed paths: M /trunk/src/c-interface.h more fixes for test_internal ------------------------------------------------------------------------ r1232 | b.lohkamp | 2008-07-08 07:45:05 +0100 (Tue, 08 Jul 2008) | 1 line Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h fixed test_internal_xx ------------------------------------------------------------------------ r1231 | pemsley | 2008-07-08 00:23:19 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Some adjustments for stringification. Maybe more portable now? ------------------------------------------------------------------------ r1230 | pemsley | 2008-07-07 21:33:02 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1229 | pemsley | 2008-07-07 21:17:21 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1228 | pemsley | 2008-07-07 21:10:52 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Add stringify for size_t. ------------------------------------------------------------------------ r1227 | pemsley | 2008-07-07 20:34:53 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/Makefile.am Put atom-quads.hh in the Makefile.am so that it gets added to the source tar. ------------------------------------------------------------------------ r1226 | pemsley | 2008-07-07 19:53:07 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1225 | pemsley | 2008-07-07 16:34:24 +0100 (Mon, 07 Jul 2008) | 3 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/c-interface-info.cc Correctly output all the chi angles of the first alt conf set in Residue Info dialog. ------------------------------------------------------------------------ r1224 | pemsley | 2008-07-07 16:15:33 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/primitive-chi-angles.cc M /trunk/ligand/rotamer-tables.cc Clean up the debugging of rotamers. ------------------------------------------------------------------------ r1223 | pemsley | 2008-07-07 16:08:22 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: A /trunk/ligand/atom-quads.hh Add atom-quads.hh ------------------------------------------------------------------------ r1222 | pemsley | 2008-07-07 16:07:48 +0100 (Mon, 07 Jul 2008) | 9 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/happy-coot-diary.html M /trunk/ligand/Makefile.am M /trunk/ligand/monomer-utils.hh M /trunk/ligand/rotamer-tables.cc M /trunk/ligand/rotamer.hh M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc A /trunk/src/testing.cc A /trunk/src/testing.hh Rework the chi-angle code. Now we don't use monomer-utils or chi-angles when getting the chi angles in probability_tables. We use primitive_chi_angles. This is so that the architecture of primitive_chi_angles and monomer_utils do not collide. Some of monomer_utils is in primitive_chi_angles now. The whole rotamer/chi-angles code needs reworking/cleaning up, but probability_tables and primitive_chi_angles are good. Added rudimentary internal testing, accessible from the scripting layer. ------------------------------------------------------------------------ r1221 | pemsley | 2008-07-07 16:01:01 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: A /trunk/ligand/primitive-chi-angles.cc A /trunk/ligand/primitive-chi-angles.hh Add new chi angle code. ------------------------------------------------------------------------ r1220 | pemsley | 2008-07-07 11:01:11 +0100 (Mon, 07 Jul 2008) | 3 lines Changed paths: A /trunk/clean-changes.sh Simple utility to remove files that were changed, but we want to discard the changes. Follow by svn update, typically. ------------------------------------------------------------------------ r1219 | pemsley | 2008-07-04 23:10:05 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.hh include math.h for lrint(). ------------------------------------------------------------------------ r1218 | b.lohkamp | 2008-07-04 18:57:12 +0100 (Fri, 04 Jul 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/Makefile.am A /trunk/python/bones_reader.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/cmtz-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h added python bones_reader added set rotamer python unittest updated glade refmac gui to incorporate TLS, SAD and TWIN refinement (not all properly functional yet) ------------------------------------------------------------------------ r1217 | pemsley | 2008-07-04 15:13:34 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add source build info to page. ------------------------------------------------------------------------ r1216 | pemsley | 2008-07-04 14:13:54 +0100 (Fri, 04 Jul 2008) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add a function to return the rotamer name give a residue spec. Needs a python version too. ------------------------------------------------------------------------ r1215 | pemsley | 2008-07-04 12:17:16 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/molecule-class-info-other.cc Add test for set-rotamer functions. ------------------------------------------------------------------------ r1214 | pemsley | 2008-07-04 11:40:46 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add functions n_rotamers() and set_residue_to_rotamer_number(). ------------------------------------------------------------------------ r1213 | pemsley | 2008-07-04 02:07:12 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple post-hoc documentation and bump the version number now that we do guile-lib build. ------------------------------------------------------------------------ r1212 | pemsley | 2008-07-03 19:38:16 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Remove the set_display_lists_for_maps(1) in mono_mode(). ------------------------------------------------------------------------ r1211 | pemsley | 2008-07-03 17:32:40 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1210 | pemsley | 2008-07-03 14:44:19 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-mmdb.cc Add string.h for memcpy() usage. ------------------------------------------------------------------------ r1209 | pemsley | 2008-07-03 14:10:21 +0100 (Thu, 03 Jul 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/ligand/monomer-utils.cc M /trunk/src/graphics-info-modelling.cc When there are alt confs in the residue, then get_chi_angles results in an inconsistency in probability_this_rotamer() in rotamer_probability_tables. Some investigation code added. ------------------------------------------------------------------------ r1208 | pemsley | 2008-07-03 13:55:25 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer-tables.cc Add string.h include file for strncmp() usage. GCC 4.3 ------------------------------------------------------------------------ r1207 | pemsley | 2008-07-03 12:48:50 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/callbacks.c Make the "draw hydrogens" in bond parameters work immediately too. ------------------------------------------------------------------------ r1206 | pemsley | 2008-07-03 12:40:26 +0100 (Thu, 03 Jul 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info.cc Make the bond width activate apply immediately (not just after "Apply" button hit). ------------------------------------------------------------------------ r1205 | pemsley | 2008-07-03 12:30:58 +0100 (Thu, 03 Jul 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Set g.bond_parameters_molecule correctly when it has not been set in wrapped_create_bond_parameters_dialog. Fixes Bill Scott bug. ------------------------------------------------------------------------ r1204 | pemsley | 2008-07-03 12:19:25 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add a function to query the state of the peptide plane restraints. ------------------------------------------------------------------------ r1203 | b.lohkamp | 2008-07-03 10:36:00 +0100 (Thu, 03 Jul 2008) | 5 lines Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py A /trunk/python/shelx_extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/08_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h added python shelx extensions refinement options dialog in extensions (py) probe dots for rotamers (if do_probe_dots_on_chis_and_rotamers) option to RSR after auto-fit-rotamer ------------------------------------------------------------------------ r1202 | pemsley | 2008-07-02 19:15:32 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1201 | b.lohkamp | 2008-07-02 18:25:18 +0100 (Wed, 02 Jul 2008) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py updated rotamer outlier test ------------------------------------------------------------------------ r1200 | pemsley | 2008-07-02 15:05:11 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Update rotamer probability test now that we have new probability tables. ------------------------------------------------------------------------ r1199 | pemsley | 2008-07-02 14:43:18 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Fix typos. ------------------------------------------------------------------------ r1198 | pemsley | 2008-07-02 14:15:48 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1197 | pemsley | 2008-07-02 14:06:48 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Make the multi-chicken colours a touch brighter. ------------------------------------------------------------------------ r1196 | pemsley | 2008-07-02 14:01:03 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add multi-chicken (lots of maps with chickenwire representation). ------------------------------------------------------------------------ r1195 | pemsley | 2008-07-02 13:32:55 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer-tables.cc More cleanups of debugging rotamer-tables usage. ------------------------------------------------------------------------ r1194 | pemsley | 2008-07-02 13:27:56 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1193 | pemsley | 2008-07-02 13:24:34 +0100 (Wed, 02 Jul 2008) | 4 lines Changed paths: M /trunk/AUTHORS M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/ligand/Makefile.am M /trunk/ligand/monomer-utils.cc A /trunk/ligand/rotamer-tables.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Several changes to add rotamer probability plots. There is a self-test of the probabilities that is run as on construction. New codes goes into rotamer-tables.cc, rather than rotamer.cc ------------------------------------------------------------------------ r1192 | pemsley | 2008-07-01 19:55:09 +0100 (Tue, 01 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/chi-angles.cc Fix typo in for OD1 in chi angle definition. ------------------------------------------------------------------------ r1191 | b.lohkamp | 2008-07-01 13:27:50 +0100 (Tue, 01 Jul 2008) | 4 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/python/coot_utils.py A /trunk/python/unittest_extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/04_cootaneer.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/Makefile.am A /trunk/python-tests/begin.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-info.cc updated python unittests reorganisation of python unittest, added unittest_extension to run one python test, a whole set of tests or all tests ------------------------------------------------------------------------ r1190 | pemsley | 2008-07-01 00:35:15 +0100 (Tue, 01 Jul 2008) | 2 lines Changed paths: A /trunk/rama-data/Makefile.am Add the Makefile.am for rama-data (sigh). ------------------------------------------------------------------------ r1189 | pemsley | 2008-06-30 15:55:58 +0100 (Mon, 30 Jun 2008) | 6 lines Changed paths: M /trunk/Makefile.am M /trunk/atom-utils/Makefile.am M /trunk/atom-utils/atom-utils.cc M /trunk/configure.in M /trunk/dnotes M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/sequence-view/Makefile.am M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.h More updates to rotamer probability. We now read them into Coot on start-up. Rotamer probabilites added to dist tar file. Canonicalize include in atom-utils and sequence-view (hopefully now it will not try to use *installed* include files when it should be reading local ones. ------------------------------------------------------------------------ r1188 | pemsley | 2008-06-30 15:41:11 +0100 (Mon, 30 Jun 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1187 | pemsley | 2008-06-30 14:29:51 +0100 (Mon, 30 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ideal/simple-restraint.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-ligand.cc Throw exception on reading the rotamer probability tables. ------------------------------------------------------------------------ r1186 | pemsley | 2008-06-30 14:00:34 +0100 (Mon, 30 Jun 2008) | 3 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h Change fix_hydrogen_names() to fix_wrapped_names() so we can fix atoms other than Hs (e.g. Os). ------------------------------------------------------------------------ r1185 | b.lohkamp | 2008-06-27 12:39:25 +0100 (Fri, 27 Jun 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/mutate.py M /trunk/python/tips.py M /trunk/python/tips_gui.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h lots of new python functions (build in and script); all scripts up to date!? fixed memory (reference counting) problem for Py_False and Py_True (hopefully) ------------------------------------------------------------------------ r1184 | pemsley | 2008-06-26 17:37:59 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh Add function write_restraints_cif_dictinary(). ------------------------------------------------------------------------ r1183 | pemsley | 2008-06-26 16:23:43 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm D /trunk/scheme/arp-warp-xml.scm M /trunk/scheme/coot.scm loop fitting updates. ------------------------------------------------------------------------ r1182 | pemsley | 2008-06-26 16:10:12 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm more updates to a-rapper-gui ------------------------------------------------------------------------ r1181 | kevin.cowtan | 2008-06-26 12:41:53 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/src/xmap-utils.cc Fix for map sigma level calculation (use doubles for summation) ------------------------------------------------------------------------ r1180 | pemsley | 2008-06-26 09:27:36 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-ligand.cc Read all the rotamer tables and add them to rotamer_probability_tables tables. ------------------------------------------------------------------------ r1179 | pemsley | 2008-06-26 07:44:02 +0100 (Thu, 26 Jun 2008) | 3 lines Changed paths: M /trunk/ligand/rotamer.cc Add stub functions for fill_chi_1_2_3 and fill_chi_1_2_3_4, so that this compiles with GCC 3.2. ------------------------------------------------------------------------ r1178 | pemsley | 2008-06-25 23:19:02 +0100 (Wed, 25 Jun 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-ligand.cc Partial updates for adding Molprobity rotamer probability tables. ------------------------------------------------------------------------ r1177 | pemsley | 2008-06-25 23:15:26 +0100 (Wed, 25 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm trivial typo fix. ------------------------------------------------------------------------ r1176 | pemsley | 2008-06-25 21:52:50 +0100 (Wed, 25 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/arp-warp-xml.scm M /trunk/src/c-interface-build.cc GUI for ARP/wARP loopy improved. replace_fragment() now correctly quotes its string in the history. ------------------------------------------------------------------------ r1175 | pemsley | 2008-06-25 17:28:29 +0100 (Wed, 25 Jun 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/refmac.scm M /trunk/src/c-interface-info.cc Add SCM and scheme code (get-refmac-version) needed to get no-labels Refmac to work. ------------------------------------------------------------------------ r1174 | pemsley | 2008-06-25 14:14:27 +0100 (Wed, 25 Jun 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add carbohdrate refinement info. ------------------------------------------------------------------------ r1173 | pemsley | 2008-06-24 19:45:26 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.hh Tinker with some code for rotamer probabilites. ------------------------------------------------------------------------ r1172 | pemsley | 2008-06-24 18:15:05 +0100 (Tue, 24 Jun 2008) | 3 lines Changed paths: M /trunk/configure.in M /trunk/macros/net-http-goosh.m4 Guile-lib is added as an extra dependency (sorry Bill :). Add a macro to test for it at configure time. ------------------------------------------------------------------------ r1171 | b.lohkamp | 2008-06-24 14:59:26 +0100 (Tue, 24 Jun 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c display skipped tests update references for About dialog clean callback.c (GTK_MAJOR_VERSION around each function) ------------------------------------------------------------------------ r1170 | pemsley | 2008-06-24 14:26:41 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/scheme/arp-warp-xml.scm Fix more types in loops-to-build line. Still loopy does not like it though. ------------------------------------------------------------------------ r1169 | pemsley | 2008-06-24 13:58:47 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/arp-warp-xml.scm Fix type in loops-to-build arg. ------------------------------------------------------------------------ r1168 | pemsley | 2008-06-24 13:56:21 +0100 (Tue, 24 Jun 2008) | 11 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ligand/ideal-rna.cc M /trunk/ligand/test-ligand.cc M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/arp-warp-xml.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/coot.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc If user specifies t in RNA, skip that residue (I will come back to make this better later). Add some starting code to test-ligand.cc to read rotamer probabilities. Add and execute test and build for guile-lib to build-its. Add a function to return the ccp4i projects to the SCM level. Add the loading of arp-warp-xml.scm, this will fail if guile-lib is not in place. Move nucleotide functions into the correct c-interfaces files. Correct map_cell_scm(), and its molecule-class-info function. Update diary. ------------------------------------------------------------------------ r1167 | pemsley | 2008-06-24 01:36:44 +0100 (Tue, 24 Jun 2008) | 7 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c fill_references_notebook argument corrected, together with GTK2 interface usage. map_parameters_scm() and map_cell_scm() function introduced initially for ARP/wARP inteface usage. Add guile-lib to build-it-gtk2-simple. Update diary. ------------------------------------------------------------------------ r1166 | pemsley | 2008-06-24 01:33:52 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/Makefile.am Add arp-warp interface to XML file. ------------------------------------------------------------------------ r1165 | pemsley | 2008-06-24 01:32:56 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: A /trunk/scheme/arp-warp-xml.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm Add ARP/wARP XML interface - first draft. ------------------------------------------------------------------------ r1164 | pemsley | 2008-06-23 17:34:58 +0100 (Mon, 23 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1163 | pemsley | 2008-06-23 17:34:37 +0100 (Mon, 23 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Add map transformation by LSQ model fit to the Extensions menu. Tidy it up a bit. ------------------------------------------------------------------------ r1162 | pemsley | 2008-06-23 15:23:08 +0100 (Mon, 23 Jun 2008) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Move functions for alignment/mutate into GUI and mutate source files (from build). Fix up align_on_chain() function. ------------------------------------------------------------------------ r1161 | pemsley | 2008-06-23 15:20:08 +0100 (Mon, 23 Jun 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/04-cootaneer.scm M /trunk/greg-tests/begin.grg factor out file->string function. Add test for align and mutate. ------------------------------------------------------------------------ r1160 | b.lohkamp | 2008-06-21 14:40:38 +0100 (Sat, 21 Jun 2008) | 1 line Changed paths: M /trunk/build-it-win fixes for windows build ------------------------------------------------------------------------ r1159 | pemsley | 2008-06-21 02:12:17 +0100 (Sat, 21 Jun 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/scheme/coot-utils.scm Update dnotes and todo. Move Centos build to 0.6. ------------------------------------------------------------------------ r1158 | pemsley | 2008-06-21 01:57:20 +0100 (Sat, 21 Jun 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Update theMapContours display list when the map is not displayed. ------------------------------------------------------------------------ r1157 | pemsley | 2008-06-20 23:44:33 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Don't do 2 backups for an eigen flip. ------------------------------------------------------------------------ r1156 | b.lohkamp | 2008-06-20 23:06:43 +0100 (Fri, 20 Jun 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/Makefile.am M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h A /trunk/src/coot-references.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/post-glade M /trunk/src/support-gtk2-extras.c M /trunk/src/support.c python gui: protect build-in functions from being overwritten add References dialog to About dialog (and fixed icon) ------------------------------------------------------------------------ r1155 | pemsley | 2008-06-20 22:16:25 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple One more go at getting the logic of testing/prerelease correct. ------------------------------------------------------------------------ r1154 | b.lohkamp | 2008-06-20 19:10:49 +0100 (Fri, 20 Jun 2008) | 1 line Changed paths: M /trunk/src/density-score-by-residue.cc move stdlib.h (Windows compile error) ------------------------------------------------------------------------ r1153 | pemsley | 2008-06-20 17:16:06 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1152 | pemsley | 2008-06-20 16:50:18 +0100 (Fri, 20 Jun 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add display on/off functionality for Ball and Stick additional reps. Changed display list handle container from a list to a vector. ------------------------------------------------------------------------ r1151 | pemsley | 2008-06-20 13:53:08 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjust the settings of running the tests again. ------------------------------------------------------------------------ r1150 | pemsley | 2008-06-20 02:13:20 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes Don't run the tests if not in york or biop. ------------------------------------------------------------------------ r1149 | pemsley | 2008-06-19 23:33:08 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/coot-close.cc M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/mol-hierachy.cc Add the ability to rotamer MSEs, by adding a function that adds extra contacts if the residue type is MSE (mmdb-extras.cc). ------------------------------------------------------------------------ r1148 | pemsley | 2008-06-19 17:19:32 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/src/c-interface.cc Add use_graphics_interface_flag protection to graphics_draw() in set_display_lists_for_maps(). ------------------------------------------------------------------------ r1147 | pemsley | 2008-06-19 13:44:38 +0100 (Thu, 19 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/density-score-by-residue.cc M /trunk/src/fix-nomenclature.cc M /trunk/src/gtk-manual.cc Further updates for 4.3, use of stdlib.h and string.h ------------------------------------------------------------------------ r1146 | pemsley | 2008-06-19 13:42:19 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/mutate.scm Updates to rapper GUI. Export 3 letter-code -> char for use by rapper gui. ------------------------------------------------------------------------ r1145 | pemsley | 2008-06-19 13:01:00 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/src/c-inner-main.c M /trunk/src/c-interface.cc From JED valgrind log, add an extra char for null termination of strings added to the preferences dir string. ------------------------------------------------------------------------ r1144 | b.lohkamp | 2008-06-19 09:45:38 +0100 (Thu, 19 Jun 2008) | 1 line Changed paths: M /trunk/scheme/ncs.scm M /trunk/src/add-c-extern.sh M /trunk/src/c-interface.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/post-gtk2-glade.sh revision in About dialog ------------------------------------------------------------------------ r1143 | pemsley | 2008-06-18 18:39:21 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple As per JED request, number the build logs in a more sensible way. ------------------------------------------------------------------------ r1142 | b.lohkamp | 2008-06-18 16:41:23 +0100 (Wed, 18 Jun 2008) | 4 lines Changed paths: M /trunk/python/ncs.py M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc M /trunk/src/post-gtk2-glade.sh fixed 'o' button in python builds include revision (and python) in About dialog (GTK2) removed bug on windows' backup_maybe() ------------------------------------------------------------------------ r1141 | pemsley | 2008-06-18 16:22:48 +0100 (Wed, 18 Jun 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Update dnotes (comment out debugging). ------------------------------------------------------------------------ r1140 | pemsley | 2008-06-18 16:21:42 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add links to python test log files. ------------------------------------------------------------------------ r1139 | b.lohkamp | 2008-06-18 12:07:17 +0100 (Wed, 18 Jun 2008) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fixed CIS pep test for missing pdb file ------------------------------------------------------------------------ r1138 | pemsley | 2008-06-18 08:59:15 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh Fix up typo, USE_PYTHON not USE_GUILE. ------------------------------------------------------------------------ r1137 | pemsley | 2008-06-18 03:00:53 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes rearrange todo list for 0.5 ------------------------------------------------------------------------ r1136 | pemsley | 2008-06-18 02:44:14 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc own_molecule_number() should also check for valid map molecule. ------------------------------------------------------------------------ r1135 | pemsley | 2008-06-18 02:42:26 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/08-utils.scm Active the molecule number test. ------------------------------------------------------------------------ r1134 | pemsley | 2008-06-18 02:38:37 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update the distribution of readline. ------------------------------------------------------------------------ r1133 | b.lohkamp | 2008-06-17 22:29:49 +0100 (Tue, 17 Jun 2008) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh more python functions, e.g. residues_near_residue_py ------------------------------------------------------------------------ r1132 | pemsley | 2008-06-17 17:47:22 +0100 (Tue, 17 Jun 2008) | 2 lines Changed paths: M /trunk/AUTHORS Add Bernhard to the Authors. ------------------------------------------------------------------------ r1131 | b.lohkamp | 2008-06-17 15:40:05 +0100 (Tue, 17 Jun 2008) | 5 lines Changed paths: M /trunk/python/generic_objects.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc all python unittest output to stdout pygtk button to show/hide all generic objects bug fix in generic_object_name_py (PYTHON BUG, not mine) side-by-side stereo -> mono resizes window to half width (GTK2) ------------------------------------------------------------------------ r1130 | pemsley | 2008-06-17 14:11:45 +0100 (Tue, 17 Jun 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Fix up hydrogens/glycosidic test typo. Throw fail if no monomer restraints in update monomer restraints test. ------------------------------------------------------------------------ r1129 | pemsley | 2008-06-17 13:55:09 +0100 (Tue, 17 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Fix glycosidic link test. ------------------------------------------------------------------------ r1128 | pemsley | 2008-06-17 05:14:37 +0100 (Tue, 17 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update to guile-1.8.5 ------------------------------------------------------------------------ r1127 | pemsley | 2008-06-16 08:49:43 +0100 (Mon, 16 Jun 2008) | 4 lines Changed paths: M /trunk/greg-tests/08-utils.scm Add begin round extra python command tests (funny, this didn't fail on some other machines). ------------------------------------------------------------------------ r1126 | pemsley | 2008-06-16 01:43:17 +0100 (Mon, 16 Jun 2008) | 10 lines Changed paths: M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/08-utils.scm M /trunk/greg-tests/begin.grg M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm M /trunk/src/graphics-info.cc Tinkerings with a-rapper-gui.scm - it runs rapper now at least and reads in output pdb file. Add python key bindings to the key bindings GUI. Add atom-match? to begin.grg. Add a tuple test to run-python-command. Add a replace-fragement test. Do not display hydrogen atoms in the intermediate atoms in refinement if they are not displayed in the "static" atoms. Update dnotes. ------------------------------------------------------------------------ r1125 | b.lohkamp | 2008-06-15 13:41:13 +0100 (Sun, 15 Jun 2008) | 1 line Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-info.cc fixed skip in unittest ------------------------------------------------------------------------ r1124 | pemsley | 2008-06-15 12:36:11 +0100 (Sun, 15 Jun 2008) | 4 lines Changed paths: M /trunk/src/c-interface.cc py_clean_internal() could return NULL, resulting in run_python_command() receiving a NULL, thus crashing. Fixed (converted to Py_None). Test added. ------------------------------------------------------------------------ r1123 | pemsley | 2008-06-15 01:41:10 +0100 (Sun, 15 Jun 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm do_colour_by_molecule_bonds() updated to add zero occupancy spots. Document flip ligand. Add "ca-trace" to rapper args. Add coot-news-info. ------------------------------------------------------------------------ r1122 | pemsley | 2008-06-13 15:48:55 +0100 (Fri, 13 Jun 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/mapview.glade M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-defines.cc M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h Fix up add-c-extern.sh to add semicolons. Fixed atom click handling checks for a fixed atom dialog before using it. Fixed atoms added for Gtk1. Release notes, diary, TODO updated. ------------------------------------------------------------------------ r1121 | pemsley | 2008-06-13 09:58:16 +0100 (Fri, 13 Jun 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1120 | pemsley | 2008-06-13 09:56:41 +0100 (Fri, 13 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm Test for SHELXL waters being added to a new chain. ------------------------------------------------------------------------ r1119 | pemsley | 2008-06-13 09:54:27 +0100 (Fri, 13 Jun 2008) | 3 lines Changed paths: M /trunk/src/globjects.cc Make the initial bond parameters molecule number invalid, so that wrapped_create_bond_parameters_dialog() no longer fails at start. ------------------------------------------------------------------------ r1118 | pemsley | 2008-06-13 09:32:06 +0100 (Fri, 13 Jun 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc Rename the residue if the residue names don't match in copy_residue_range() for ncs fragments. ------------------------------------------------------------------------ r1117 | pemsley | 2008-06-13 09:30:38 +0100 (Fri, 13 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/07-ncs.scm Add mutate residue test to NCS copy region test. ------------------------------------------------------------------------ r1116 | b.lohkamp | 2008-06-13 09:30:35 +0100 (Fri, 13 Jun 2008) | 3 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/Makefile.am M /trunk/python-tests/coot_unittest.py M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-render.cc more unittests, add coot_unittest to Makefile.am some improvements to povray ------------------------------------------------------------------------ r1115 | pemsley | 2008-06-12 23:10:58 +0100 (Thu, 12 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/ncs.scm M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Fix the the apply_ncs_to_view_orientation function in the case of NCS with a heterodimer (fixes Phil's problem?) ------------------------------------------------------------------------ r1114 | pemsley | 2008-06-12 21:35:35 +0100 (Thu, 12 Jun 2008) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/gdk-keysym.awk M /trunk/coot-utils/gdk-keysyms.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/08-utils.scm M /trunk/greg-tests/begin.grg M /trunk/scheme/ncs.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h Add draw_ncs_ghost_state() function. Add has-term-atom? function to begin.grg, used to test if a residue has a TER record. TER records are removed from C-terminii on adding a terminal residue. Need to update terminal residue addition test pdb. Add non-alpha-numeric key codes. Extra key code tests. Add test for residues near residue. ------------------------------------------------------------------------ r1113 | pemsley | 2008-06-12 00:51:24 +0100 (Thu, 12 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add "pukka puckers?" gui to the validation menu. ------------------------------------------------------------------------ r1112 | b.lohkamp | 2008-06-11 17:12:35 +0100 (Wed, 11 Jun 2008) | 1 line Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple python test only run if build with python ------------------------------------------------------------------------ r1111 | b.lohkamp | 2008-06-11 17:02:54 +0100 (Wed, 11 Jun 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils.cc M /trunk/src/graphics-info-render.cc better povray clipping and avoid view angles > 180 python testing in build-it and build-it-gtk2-simple ------------------------------------------------------------------------ r1110 | b.lohkamp | 2008-06-11 15:07:43 +0100 (Wed, 11 Jun 2008) | 4 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/python/group_settings.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc python molprobity fixes fix empty residue type selection returning valid imol, but not valid molecule test for empty residue type selection (python/scheme) ------------------------------------------------------------------------ r1109 | b.lohkamp | 2008-06-10 12:38:51 +0100 (Tue, 10 Jun 2008) | 1 line Changed paths: M /trunk/build-it-win M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info.h fix for font in sequence view and CCP4 directory in file selection ------------------------------------------------------------------------ r1108 | pemsley | 2008-06-10 08:20:14 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm Adjust these closing of maps in the shelx tests. ------------------------------------------------------------------------ r1107 | pemsley | 2008-06-10 08:14:58 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-waters.cc Add bad model and map protection. ------------------------------------------------------------------------ r1106 | pemsley | 2008-06-10 02:00:15 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: A /trunk/coot-utils/coot-coord-utils-nucleotides.cc A /trunk/src/c-interface-nucleotides.cc Add missing files. ------------------------------------------------------------------------ r1105 | pemsley | 2008-06-10 01:58:47 +0100 (Tue, 10 Jun 2008) | 9 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot-align.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add pucker analysis (at a deep level, scripting but not GUI). Add function to convert to a residue_spec_t from a SCM object. Start throwing exceptions. c-interface-nucleotides.cc coot-coord-utils-nucleotides.cc introduced. On addition of waters (find-waters) to a shelx molecule, set the atom occupancy to 11.0 Make a function get_following_residue() (c.f. get_residue()). utils lsq_plane_deviation now returns the rms deviation of the plane too. ------------------------------------------------------------------------ r1104 | pemsley | 2008-06-10 01:52:44 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-waters.cc Add no graphics protection. ------------------------------------------------------------------------ r1103 | pemsley | 2008-06-10 01:51:45 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/begin.grg Add test for adding waters to shelx molecule. Factor out shelxl water test. ------------------------------------------------------------------------ r1102 | pemsley | 2008-06-09 17:35:12 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc Move reset_view(). ------------------------------------------------------------------------ r1101 | b.lohkamp | 2008-06-09 17:32:35 +0100 (Mon, 09 Jun 2008) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h removable glob extensions; fix font width in seq view fixed?! ------------------------------------------------------------------------ r1100 | pemsley | 2008-06-09 17:27:45 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Add restraint updating test. ------------------------------------------------------------------------ r1099 | pemsley | 2008-06-09 17:25:01 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Update release notes. ------------------------------------------------------------------------ r1098 | pemsley | 2008-06-09 17:24:00 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Fix typo. ------------------------------------------------------------------------ r1097 | b.lohkamp | 2008-06-09 14:52:14 +0100 (Mon, 09 Jun 2008) | 6 lines Changed paths: M /trunk/build-it-win M /trunk/ligand/test-helix-placement.cc M /trunk/python/refmac.py M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c ligand/test-helix-placement.cc src/c-interface.cc src/c-interface-validate.cc src/callbacks.c build-it-win ------------------------------------------------------------------------ r1096 | pemsley | 2008-06-08 23:46:50 +0100 (Sun, 08 Jun 2008) | 3 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for applying sequence info in Add Terminal Residue and reading in the pdb file after it has had hydrogens added. ------------------------------------------------------------------------ r1095 | pemsley | 2008-06-07 14:20:19 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add hilighting function - using residues-near-residue. ------------------------------------------------------------------------ r1094 | pemsley | 2008-06-07 14:19:24 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1093 | pemsley | 2008-06-07 14:18:55 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Notes for simple build-it. ------------------------------------------------------------------------ r1092 | pemsley | 2008-06-07 14:17:33 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add show hydrogens state function. ------------------------------------------------------------------------ r1091 | pemsley | 2008-06-07 14:15:12 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Update smooth recentering documentation. ------------------------------------------------------------------------ r1090 | pemsley | 2008-06-07 09:41:44 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Bump up the version of Python to 2.5.2 ------------------------------------------------------------------------ r1089 | pemsley | 2008-06-06 23:07:51 +0100 (Fri, 06 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h In active_atom_spec(), pick only atoms that are pickable. ------------------------------------------------------------------------ r1088 | pemsley | 2008-06-06 21:21:25 +0100 (Fri, 06 Jun 2008) | 2 lines Changed paths: A /trunk/rama-data A /trunk/rama-data/rama500-general.data A /trunk/rama-data/rama500-gly-sym.data A /trunk/rama-data/rama500-prepro.data A /trunk/rama-data/rama500-pro.data A /trunk/rama-data/rota500-arg.data A /trunk/rama-data/rota500-asn.data A /trunk/rama-data/rota500-asp.data A /trunk/rama-data/rota500-cys.data A /trunk/rama-data/rota500-gln.data A /trunk/rama-data/rota500-glu.data A /trunk/rama-data/rota500-his.data A /trunk/rama-data/rota500-ile.data A /trunk/rama-data/rota500-leu.data A /trunk/rama-data/rota500-lys.data A /trunk/rama-data/rota500-met.data A /trunk/rama-data/rota500-phetyr.data A /trunk/rama-data/rota500-pro.data A /trunk/rama-data/rota500-ser.data A /trunk/rama-data/rota500-thr.data A /trunk/rama-data/rota500-trp.data A /trunk/rama-data/rota500-val.data Add rotamer probabilities from Molprobity. ------------------------------------------------------------------------ r1087 | pemsley | 2008-06-05 17:41:57 +0100 (Thu, 05 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/shelx-extensions.scm Update, by adding a filter function the use of generic-chooser-and-file-selection in shelx-extensions.scm. ------------------------------------------------------------------------ r1086 | pemsley | 2008-06-05 14:14:03 +0100 (Thu, 05 Jun 2008) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-extras.cc M /trunk/coot-surface/rgbreps.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/test-utils.cc M /trunk/cootaneer/buccaneer-prot.cpp M /trunk/cootaneer/cootaneer-sequence.cpp M /trunk/db-main/db-main.cc M /trunk/db-main/testdbmain.cc M /trunk/db-main/train-pepflip.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/test-geometry.cc M /trunk/high-res/globularize.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/monomer-utils.cc M /trunk/ligand/test-helix-placement.cc M /trunk/ligand/test-ligand.cc M /trunk/mini-mol/mini-mol.cc M /trunk/skeleton/BuildCas.cc M /trunk/surface/CXXFortranFile.cpp Small fixes from porting to GCC 4.3. Fixes sort(),reverse()/algorithm, abs() no longer returns an int - now use stdlib.h and labs(). atof()/stdlib, strcp and other string functions in string.h, ------------------------------------------------------------------------ r1085 | pemsley | 2008-06-05 12:33:58 +0100 (Thu, 05 Jun 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc Change default number of step on smooth scrolling from 80 to 40. ------------------------------------------------------------------------ r1084 | pemsley | 2008-06-05 04:11:40 +0100 (Thu, 05 Jun 2008) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/test-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Sort chains function added coot util, but deleting chain causes crash. Sort chains test added but not used yet. Residues near residue function added. Add c-interface.h documentation for delete_checked_waters_baddies(). Documentation for raster3d bones. ------------------------------------------------------------------------ r1083 | pemsley | 2008-06-02 10:31:19 +0100 (Mon, 02 Jun 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Properly pad the UNIT line with 0s to the size of the SFAC line. ------------------------------------------------------------------------ r1082 | pemsley | 2008-06-01 18:00:28 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/c-interface-build.cc Go To Atom dialog is properly updated on merging molecules. ------------------------------------------------------------------------ r1081 | pemsley | 2008-06-01 17:16:28 +0100 (Sun, 01 Jun 2008) | 4 lines Changed paths: M /trunk/scheme/generic-objects.scm M /trunk/src/molecule-class-info-mutate.cc Add a user variable reduce-molecule-updates-current, that when set makes the output of reduce overwrite the probed molecule (not create a new one). ------------------------------------------------------------------------ r1080 | pemsley | 2008-06-01 17:13:55 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh Put the SFAC line before the UNIT line in shelxl output. ------------------------------------------------------------------------ r1079 | pemsley | 2008-06-01 12:36:11 +0100 (Sun, 01 Jun 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-mutate.cc Remember the scroll wheel map in the state file. Don't monkey with the alignment score (now back to defaults and alignment gets both (test) N an C term alignment correct). ------------------------------------------------------------------------ r1078 | pemsley | 2008-06-01 11:34:08 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-state.cc Add to the state file, the setting for the refinement map. ------------------------------------------------------------------------ r1077 | pemsley | 2008-06-01 03:57:41 +0100 (Sun, 01 Jun 2008) | 10 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h Add function to set the scroll wheel map. Add functions to print a residue spec, and to compare residue specs. Extend alignment class to add insertions at the C terminus. Add code to get the terminal residue type by sequence alignment. Change from char *get_pkgdatadir() to PyObject *get_pkgdatadir_py(), fixes a bug. Added find_terminal_residue_type() function used for testing. Change the default graphics_info_t::add_terminal_residue_type from "ALA" to "auto". ------------------------------------------------------------------------ r1076 | pemsley | 2008-06-01 03:52:08 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm add shelx-extensions.scm to installed files. ------------------------------------------------------------------------ r1075 | pemsley | 2008-06-01 03:51:10 +0100 (Sun, 01 Jun 2008) | 3 lines Changed paths: M /trunk/python/coot_utils.py Take out verbiage on key pressing, but not found in python list. add get_pkgdatadir() redefinition. ------------------------------------------------------------------------ r1074 | pemsley | 2008-05-29 22:57:08 +0100 (Thu, 29 May 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc Enable double clicking to label for symmetry atoms. ------------------------------------------------------------------------ r1073 | pemsley | 2008-05-28 19:48:00 +0100 (Wed, 28 May 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Fix change of drawing style on modifying a molecule in CA+ligs representation. ------------------------------------------------------------------------ r1072 | pemsley | 2008-05-28 19:04:20 +0100 (Wed, 28 May 2008) | 7 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/03-ligand.scm M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add flip-ligand function. Should be bound to a key. Added test for above. Fixed extra parameters to additional represenations in the state file. Fix up the GUI reading for ball and stick add reps. molecule-number-list updated to use range. update dnotes and TODO. ------------------------------------------------------------------------ r1071 | pemsley | 2008-05-28 14:29:05 +0100 (Wed, 28 May 2008) | 3 lines Changed paths: M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/08-utils.scm skip the molecule number test for now - Hmm.. In the ligand test, don't make 50 copies any more - make 5. ------------------------------------------------------------------------ r1070 | pemsley | 2008-05-27 18:40:58 +0100 (Tue, 27 May 2008) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h own_molecule_number() introduced for testing consistency of internal and external molecule numbers. ------------------------------------------------------------------------ r1069 | pemsley | 2008-05-27 18:39:49 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Some notes for baton building. ------------------------------------------------------------------------ r1068 | pemsley | 2008-05-27 18:39:13 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Tidy up SCM usage. ------------------------------------------------------------------------ r1067 | pemsley | 2008-05-27 18:36:56 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/TODO More TODOs. ------------------------------------------------------------------------ r1066 | pemsley | 2008-05-27 18:36:03 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/dnotes upate dnotes. ------------------------------------------------------------------------ r1065 | pemsley | 2008-05-27 17:53:58 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/08-utils.scm Add molecule number consistency test at teh end of utils section. ------------------------------------------------------------------------ r1064 | pemsley | 2008-05-27 16:27:17 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Increase the vertical size of the atoms window in residue info dialog. ------------------------------------------------------------------------ r1063 | pemsley | 2008-05-27 16:15:26 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/src/graphics-info-superpose.cc Re-order TODO list. ------------------------------------------------------------------------ r1062 | pemsley | 2008-05-27 16:14:16 +0100 (Tue, 27 May 2008) | 3 lines Changed paths: M /trunk/src/c-interface-superpose.cc Add a menu to the chain option menu in superpose dialog, so that we don't get "gtk_menu_get_active: assertion `GTK_IS_MENU (menu)' failed" ------------------------------------------------------------------------ r1061 | pemsley | 2008-05-27 16:12:22 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add flying hydrogens post-undo test. ------------------------------------------------------------------------ r1060 | pemsley | 2008-05-27 16:10:55 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm Some more progress on rapper gui. Doesn't work yet - problem with params.xml ------------------------------------------------------------------------ r1059 | pemsley | 2008-05-27 16:10:06 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Fix typo in skeletonization docs. ------------------------------------------------------------------------ r1058 | pemsley | 2008-05-26 11:19:34 +0100 (Mon, 26 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/geometry-graphs.cc Punt the smooth icon rendering. ------------------------------------------------------------------------ r1057 | b.lohkamp | 2008-05-25 17:32:40 +0100 (Sun, 25 May 2008) | 1 line Changed paths: M /trunk/src/graphics-info-superpose.cc fixed doublication of imol in SSM superpose ------------------------------------------------------------------------ r1056 | pemsley | 2008-05-22 17:15:02 +0100 (Thu, 22 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm New glycosidic bond test (new test pdb file). ------------------------------------------------------------------------ r1055 | pemsley | 2008-05-22 17:14:30 +0100 (Thu, 22 May 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Correct fix for A-L.cif (etc) file reading from monomer library. ------------------------------------------------------------------------ r1054 | pemsley | 2008-05-22 16:10:18 +0100 (Thu, 22 May 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc Try to read A-L.cif if a-L.cif fails. Same for B-D.cif and b-D.cif. Does this fix the glyosidic bond test? ------------------------------------------------------------------------ r1053 | pemsley | 2008-05-22 11:24:47 +0100 (Thu, 22 May 2008) | 3 lines Changed paths: M /trunk/src/restraints-editor.cc Fix up error reading plane restraints when there are plane restraints with different number of atoms. ------------------------------------------------------------------------ r1052 | pemsley | 2008-05-22 00:13:42 +0100 (Thu, 22 May 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo in status file name. ------------------------------------------------------------------------ r1051 | pemsley | 2008-05-21 15:58:55 +0100 (Wed, 21 May 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Update build analysis page to get correct tar files (fixes bug on introduction of bins links from WinCoot build). ------------------------------------------------------------------------ r1050 | pemsley | 2008-05-21 14:34:59 +0100 (Wed, 21 May 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add representation_type arg to addition_representation_args (so that we can specify ball and stick, simple lines, etc). ------------------------------------------------------------------------ r1049 | pemsley | 2008-05-20 20:39:28 +0100 (Tue, 20 May 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1048 | pemsley | 2008-05-20 20:33:51 +0100 (Tue, 20 May 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1047 | pemsley | 2008-05-20 17:25:20 +0100 (Tue, 20 May 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/src/molecule-class-info.cc Use write_atom_selection_file() not atom_sel.mol->WritePDBASCII() in make_backup(). Fixes problem of renaming hydrogens on undo. ------------------------------------------------------------------------ r1046 | pemsley | 2008-05-20 10:03:22 +0100 (Tue, 20 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Add bond length test for glycosidic linkage. ------------------------------------------------------------------------ r1045 | pemsley | 2008-05-19 14:29:58 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Change the distance for finding glycosidic linkage to 3.0A. ------------------------------------------------------------------------ r1044 | b.lohkamp | 2008-05-19 13:29:54 +0100 (Mon, 19 May 2008) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc python scripting for refmac NCS and rigid body groups ------------------------------------------------------------------------ r1043 | pemsley | 2008-05-19 12:19:41 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Revert coot-crash-catcher.scm to how it used to be. ------------------------------------------------------------------------ r1042 | pemsley | 2008-05-19 08:06:37 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/dnotes Resolve updates. ------------------------------------------------------------------------ r1041 | pemsley | 2008-05-19 07:40:33 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Markup in progress build-result in grey. ------------------------------------------------------------------------ r1040 | pemsley | 2008-05-19 07:19:05 +0100 (Mon, 19 May 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/gtk-manual.hh M /trunk/src/molecule-class-info.cc Additional representations frame is not shown if there are no add reps. Additional representations frame dynamically updated and shown on addition of a add rep. Fix crash on pressing space with no molecules shown. Recentre on reading a shelx molecule. ------------------------------------------------------------------------ r1039 | pemsley | 2008-05-19 06:23:28 +0100 (Mon, 19 May 2008) | 3 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-crash-catcher.scm M /trunk/scheme/coot-gui.scm Add ARP/wARP interface to the loop builder (not filled yet). Add transform-map-using-lsq-matrix-gui. ------------------------------------------------------------------------ r1038 | pemsley | 2008-05-18 13:16:28 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Update the build and test status, so that we can tell the difference between an in-progress build and a failed build. ------------------------------------------------------------------------ r1037 | pemsley | 2008-05-18 09:50:45 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/callbacks.c M /trunk/src/molecule-class-info.cc Don't delete the menu in fill_place_atom_molecule_option_menu() if the menu is null (as it always is for GTK2, I think). ------------------------------------------------------------------------ r1036 | pemsley | 2008-05-18 09:39:51 +0100 (Sun, 18 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r1035 | pemsley | 2008-05-18 09:38:00 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info.cc Updates to get the correct residue number and SFAC when a new atom is added to a shelx molecule. ------------------------------------------------------------------------ r1034 | pemsley | 2008-05-18 09:36:24 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh Updates for handling SFAC updates when a new atom type is introduced into a shelx molecule. ------------------------------------------------------------------------ r1033 | b.lohkamp | 2008-05-15 16:32:15 +0100 (Thu, 15 May 2008) | 8 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/refmac.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/cmtz-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h added some new python extensions fixed selection of molecules in python coot_gui fixed crash if HOME had "/" at the end new refmac GUI (for gtk2): - refinement options - phase combination with phi&fom and hl (only works for python currently) - NCS button (needs to made functional...) ------------------------------------------------------------------------ r1032 | pemsley | 2008-05-14 23:16:09 +0100 (Wed, 14 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add no-graphics protection to set_display_lists_for_maps(). ------------------------------------------------------------------------ r1031 | pemsley | 2008-05-14 05:11:28 +0100 (Wed, 14 May 2008) | 6 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ligand/chi-angles.cc M /trunk/ligand/ideal-rna.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h The torsion angles are better handled now, incorporating the correct handling of const angles in edit chi. And maybe wiggly ligands too. Investigation/debugging add to ideal nucleic acids. Clear Ball&Stick added to Extensions. Update validation graphs on delete water and residue. ------------------------------------------------------------------------ r1030 | pemsley | 2008-05-13 07:17:07 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm map-sigma wrapper. ------------------------------------------------------------------------ r1029 | pemsley | 2008-05-13 07:12:57 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/scheme/generic-objects.scm Use -oldbpdb arg when running reduce. ------------------------------------------------------------------------ r1028 | pemsley | 2008-05-13 07:11:40 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/scheme/povray.scm update to povray 3.6 (actually, make it user-setable now). ------------------------------------------------------------------------ r1027 | pemsley | 2008-05-13 06:55:36 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add map sigma test. ------------------------------------------------------------------------ r1026 | pemsley | 2008-05-13 06:31:05 +0100 (Tue, 13 May 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Fix problem of messing with display lists when not using graphics (found from running tests on a mac). ------------------------------------------------------------------------ r1025 | pemsley | 2008-05-13 05:37:44 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface.h Add map_sigma() function (combined with previous commit). ------------------------------------------------------------------------ r1024 | pemsley | 2008-05-13 05:36:52 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add no graphics protection to set_background_colour(). ------------------------------------------------------------------------ r1023 | pemsley | 2008-05-12 21:12:01 +0100 (Mon, 12 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix ups to get the url of the WinCoot binary correct. ------------------------------------------------------------------------ r1022 | pemsley | 2008-05-12 01:15:10 +0100 (Mon, 12 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Updates to find bernhard's WinCoot binary builds. ------------------------------------------------------------------------ r1021 | b.lohkamp | 2008-05-09 10:24:37 +0100 (Fri, 09 May 2008) | 1 line Changed paths: M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc more windows directory/backup fixes ------------------------------------------------------------------------ r1020 | b.lohkamp | 2008-05-08 10:03:14 +0100 (Thu, 08 May 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows build script ------------------------------------------------------------------------ r1019 | b.lohkamp | 2008-05-06 20:17:46 +0100 (Tue, 06 May 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc more windows directory fixes, esp. for backup and recover session. recover session checks if COOT_BACKUP_DIR exists now. ------------------------------------------------------------------------ r1018 | b.lohkamp | 2008-05-06 15:29:19 +0100 (Tue, 06 May 2008) | 1 line Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/python/coot_utils.py M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/main.cc Windows directory fixes ------------------------------------------------------------------------ r1017 | pemsley | 2008-05-04 12:57:47 +0100 (Sun, 04 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Enable the display of WinCoot build. ------------------------------------------------------------------------ r1016 | pemsley | 2008-05-03 23:55:00 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use guile version 1.8.4 ------------------------------------------------------------------------ r1015 | pemsley | 2008-05-03 23:36:32 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Apply -ne -> != fix from Joseph Moran. ------------------------------------------------------------------------ r1014 | pemsley | 2008-05-03 23:31:46 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/build-it-win Make the win coot build test output to gtk2-test.log (with optional guile). ------------------------------------------------------------------------ r1013 | pemsley | 2008-05-03 18:10:35 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/mapview.glade M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-info.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.cc M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h Minor adjustments to get gtk1 version to compile. ------------------------------------------------------------------------ r1012 | b.lohkamp | 2008-05-03 17:08:24 +0100 (Sat, 03 May 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py A /trunk/python/remote_control.py M /trunk/src/c-interface.cc M /trunk/src/c-interface.h remote control for python (not properly working yet) ------------------------------------------------------------------------ r1011 | pemsley | 2008-05-03 14:07:15 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/rama_plot.cc M /trunk/src/restraints-editor.cc Fix resizing of the other GL context in side by side stereo mode. ------------------------------------------------------------------------ r1010 | pemsley | 2008-05-03 14:03:02 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm Rework the key binding GUI, to display already-existing key bindings. ------------------------------------------------------------------------ r1009 | pemsley | 2008-05-02 11:27:17 +0100 (Fri, 02 May 2008) | 2 lines Changed paths: M /trunk/python/coot_toolbuttons.py Add pixmaps to pixbuf_dir. ------------------------------------------------------------------------ r1008 | pemsley | 2008-05-01 23:47:56 +0100 (Thu, 01 May 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm Couple of fixes to key bindings. Fix error when key not found. Improve display of keybindings in dialog. ------------------------------------------------------------------------ r1007 | pemsley | 2008-05-01 09:48:01 +0100 (Thu, 01 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add back the format line which makes the key bindings work again. ------------------------------------------------------------------------ r1006 | pemsley | 2008-05-01 08:57:18 +0100 (Thu, 01 May 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1005 | pemsley | 2008-05-01 08:47:24 +0100 (Thu, 01 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/happy-coot-diary.html Dragon is doing the F8 builds currently. ------------------------------------------------------------------------ r1004 | b.lohkamp | 2008-04-29 13:34:52 +0100 (Tue, 29 Apr 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/python-tests/08_utils.py M /trunk/scheme/refmac.scm M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h refmac can be run without setting column labels ------------------------------------------------------------------------ r1003 | pemsley | 2008-04-28 20:23:39 +0100 (Mon, 28 Apr 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1002 | pemsley | 2008-04-28 17:16:24 +0100 (Mon, 28 Apr 2008) | 2 lines Changed paths: M /trunk/src/restraints-editor.cc Fix make_tree_store_for_planes in the case of 24 (not 14) atoms. ------------------------------------------------------------------------ r1001 | pemsley | 2008-04-28 15:57:16 +0100 (Mon, 28 Apr 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Apply Joseph Moran's fix correctly. ------------------------------------------------------------------------ r1000 | pemsley | 2008-04-28 14:51:18 +0100 (Mon, 28 Apr 2008) | 5 lines Changed paths: M /trunk/README M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2 M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/greg-tests/08-utils.scm M /trunk/happy-coot-diary.html M /trunk/ligand/dunbrack.cc M /trunk/mapview.glade M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-defines.cc M /trunk/src/main.cc Add a function coot_has_python_p() and schemey version. Cootaneer renamed and will use the python version, if available. Fix gtk1 add reps group for checkbuttons. Trivial clean ups. ------------------------------------------------------------------------ r999 | b.lohkamp | 2008-04-28 10:24:11 +0100 (Mon, 28 Apr 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py fixed cootaneer tree path problem ------------------------------------------------------------------------ r998 | b.lohkamp | 2008-04-28 09:49:26 +0100 (Mon, 28 Apr 2008) | 6 lines Changed paths: M /trunk/python/Makefile.am A /trunk/python/brute_lsqman.py A /trunk/python/clear_backup.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-inner-main.c M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/main.cc avoid loading toolbutton preferences when no-graphics coot_toolbuttons picks up pkgdatadir if COOT_PIX_BUFFER is not defined improved file handling in coot_unittest.py clear_backup.py in again add brute_lsqman.py ------------------------------------------------------------------------ r997 | pemsley | 2008-04-27 09:30:02 +0100 (Sun, 27 Apr 2008) | 2 lines Changed paths: M /trunk/greg-tests/08-utils.scm Update key bindings test, now that we pass a binding name. ------------------------------------------------------------------------ r996 | pemsley | 2008-04-25 22:28:46 +0100 (Fri, 25 Apr 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. first for a long time. ------------------------------------------------------------------------ r995 | pemsley | 2008-04-25 22:01:09 +0100 (Fri, 25 Apr 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html New Oxfordian Happy Coot diary. ------------------------------------------------------------------------ r994 | pemsley | 2008-04-25 21:26:49 +0100 (Fri, 25 Apr 2008) | 2 lines Changed paths: M /trunk/python-tests/Makefile.am Fix 07_ncs.py typo. ------------------------------------------------------------------------ r993 | pemsley | 2008-04-25 17:18:18 +0100 (Fri, 25 Apr 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Rework the web page builder, accounting for pythonic builds and rearranging build hosts. ------------------------------------------------------------------------ r992 | pemsley | 2008-04-25 16:56:23 +0100 (Fri, 25 Apr 2008) | 5 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add a name to the key binding mechanism. Add New molecule by sphere to gui. Change the name of Cootaneer. Add primitive gui to show key bindings. ------------------------------------------------------------------------ r991 | b.lohkamp | 2008-04-25 08:56:57 +0100 (Fri, 25 Apr 2008) | 1 line Changed paths: M /trunk/python/Makefile.am remove clear_backup.py from makefile ------------------------------------------------------------------------ r990 | pemsley | 2008-04-24 11:32:04 +0100 (Thu, 24 Apr 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Test python against the installation version, not the system version. ------------------------------------------------------------------------ r989 | b.lohkamp | 2008-04-24 08:53:46 +0100 (Thu, 24 Apr 2008) | 3 lines Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python/exercise_python_mol.py M /trunk/python-tests/01_pdb_mtz.py A /trunk/python-tests/08_utils.py M /trunk/python-tests/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/main.cc added python module clear_backup.py and test 08_utils.py various python fixes ------------------------------------------------------------------------ r988 | pemsley | 2008-04-23 23:04:37 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm No longer build for FC6 on bragg1. ------------------------------------------------------------------------ r987 | pemsley | 2008-04-23 22:01:27 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/build-it diagnose build_type problems. ------------------------------------------------------------------------ r986 | pemsley | 2008-04-23 20:45:35 +0100 (Wed, 23 Apr 2008) | 3 lines Changed paths: M /trunk/build-it More tinkering with the build and test status files for gtk1 build to separate out the python build statuses. ------------------------------------------------------------------------ r985 | pemsley | 2008-04-23 20:20:27 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/build-it Change the file name target for the build and test log file. ------------------------------------------------------------------------ r984 | pemsley | 2008-04-23 19:51:45 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/interface.c remove some debugging. ------------------------------------------------------------------------ r983 | b.lohkamp | 2008-04-23 11:44:45 +0100 (Wed, 23 Apr 2008) | 1 line Changed paths: A /trunk/python/example_python_mol_representation.py A /trunk/python/exercise_python_mol.py add python modules ------------------------------------------------------------------------ r982 | b.lohkamp | 2008-04-22 09:40:22 +0100 (Tue, 22 Apr 2008) | 1 line Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh py_to_scm (and scm_to_py) fixed ------------------------------------------------------------------------ r981 | b.lohkamp | 2008-04-22 08:39:56 +0100 (Tue, 22 Apr 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows build script ------------------------------------------------------------------------ r980 | pemsley | 2008-04-21 21:28:19 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/fascinating-things.scm Fix up the fascintating things. Test junk has been left lying around. ------------------------------------------------------------------------ r979 | pemsley | 2008-04-21 21:23:41 +0100 (Mon, 21 Apr 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/geometry/protein-geometry.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/restraints-editor-c.h M /trunk/src/restraints-editor.cc Add a save restraints option to the residue editor. Remove some debugging output. ------------------------------------------------------------------------ r978 | pemsley | 2008-04-21 14:15:54 +0100 (Mon, 21 Apr 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Only set the active text item if we have get_active text for a combo box. (ifdef outs on Gtk1 build). ------------------------------------------------------------------------ r977 | pemsley | 2008-04-21 14:08:03 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gui.cc Set the active item for the additional representation bond width. ------------------------------------------------------------------------ r976 | pemsley | 2008-04-21 13:51:35 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Set the first entry in the restraints editor type selector (ALA, typically). ------------------------------------------------------------------------ r975 | pemsley | 2008-04-21 10:10:36 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-gtk2.glade M /trunk/dnotes D /trunk/restraints-editor/src/restraints-editor.cc D /trunk/restraints-editor/src/restraints-editor.hh M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/interface.h A /trunk/src/restraints-editor-c.h A /trunk/src/restraints-editor.cc (from /trunk/restraints-editor/src/restraints-editor.cc:966) A /trunk/src/restraints-editor.hh (from /trunk/restraints-editor/src/restraints-editor.hh:970) Big updates to the restraints editor. Merge it into the main line. ------------------------------------------------------------------------ r974 | pemsley | 2008-04-21 10:08:04 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c New gtk2 interface - residue editor and with names. ------------------------------------------------------------------------ r973 | pemsley | 2008-04-21 05:46:50 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add monomer_types function. ------------------------------------------------------------------------ r972 | pemsley | 2008-04-20 23:06:19 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix typo. ------------------------------------------------------------------------ r971 | pemsley | 2008-04-20 22:48:52 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot.scm M /trunk/scheme/fascinating-things.scm Add fascintating-things to the loaded files. ------------------------------------------------------------------------ r970 | pemsley | 2008-04-20 22:30:23 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/restraints-editor/src/restraints-editor.hh updates to restraints-editor.hh. It will be moved shortly. ------------------------------------------------------------------------ r969 | pemsley | 2008-04-20 20:18:03 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Put a limit to the size of the red bars. ------------------------------------------------------------------------ r968 | b.lohkamp | 2008-04-18 21:32:49 +0100 (Fri, 18 Apr 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/python/coot_gui.py M /trunk/python/refmac.py M /trunk/src/c-interface-preferences.cc some Windows directory fixes python scripting function to start widgets in threads (used in read_refmac_log) ------------------------------------------------------------------------ r967 | pemsley | 2008-04-18 08:48:01 +0100 (Fri, 18 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Don't test on the 0th element of a python list in py_to_scm(). ------------------------------------------------------------------------ r966 | pemsley | 2008-04-17 23:20:57 +0100 (Thu, 17 Apr 2008) | 6 lines Changed paths: M /trunk/autogen.sh M /trunk/config.guess M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh Add scm_to_py and py_to_scm. They are broken though when used with run_scheme_command and run_python_command(). run_scheme_command fails when there is a parenetheses mismatch. run_python_command fails when given a python list. However, run_scheme_command works with a scheme list. ------------------------------------------------------------------------ r965 | pemsley | 2008-04-17 21:09:26 +0100 (Thu, 17 Apr 2008) | 2 lines Changed paths: A /trunk/restraints-editor/Makefile.am M /trunk/restraints-editor/src/Makefile.am A /trunk/restraints-editor/src/callbacks.c A /trunk/restraints-editor/src/callbacks.h A /trunk/restraints-editor/src/post-glade A /trunk/restraints-editor/src/post-gtk2-glade.sh A /trunk/restraints-editor/src/restraints-editor-c.h A /trunk/restraints-editor/src/restraints-editor.cc A /trunk/restraints-editor/src/restraints-editor.hh Add the restraints editor (0.5) to the repo. ------------------------------------------------------------------------ r964 | b.lohkamp | 2008-04-17 17:56:01 +0100 (Thu, 17 Apr 2008) | 5 lines Changed paths: A /trunk/python/a_rapper_gui.py M /trunk/python/coot_utils.py M /trunk/python/libcheck.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/06_ssm.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-other.cc added run_python_command and run_scheme_command added missing Py_DECREF (maybe too many...) fix libcheck.py and some unittests added a_rapper_gui.py (not fully functional yet, hence not in Makefile.am yet) ------------------------------------------------------------------------ r963 | kevin.cowtan | 2008-04-17 17:04:15 +0100 (Thu, 17 Apr 2008) | 4 lines Changed paths: M /trunk/src/molecule-class-info.cc Add Polar and Euler representations (+ translation) when transforming a molecule. Useful for SSM and NCS - e.g. can get operators for another program. ------------------------------------------------------------------------ r962 | pemsley | 2008-04-17 12:23:35 +0100 (Thu, 17 Apr 2008) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add the ability to write a cif restraints to a dictionary_residue_resetraint. Not quite working because the MMCIFData DataName is getting overwritten. Perhaps I need a cif category or some such. ------------------------------------------------------------------------ r961 | pemsley | 2008-04-16 18:40:19 +0100 (Wed, 16 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add a write_cif() stub function to dictionary_residue_restraints_t class. ------------------------------------------------------------------------ r960 | b.lohkamp | 2008-04-14 11:25:15 +0100 (Mon, 14 Apr 2008) | 3 lines Changed paths: M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/tips.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh pythonized goto_next/prev_atom_maybe some bug fixes in python unittest and python modules ------------------------------------------------------------------------ r959 | pemsley | 2008-04-13 11:00:16 +0100 (Sun, 13 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add line tellling us where the std output has been redirected. ------------------------------------------------------------------------ r958 | pemsley | 2008-04-12 15:38:47 +0100 (Sat, 12 Apr 2008) | 5 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc stop echoing rsync lines in build log. clean build and test status before starting. Rework the saving of the worst satisfied restraint in a residue. Rework switching of stereo modes. ------------------------------------------------------------------------ r957 | pemsley | 2008-04-09 13:04:56 +0100 (Wed, 09 Apr 2008) | 4 lines Changed paths: M /trunk/greg-tests/03-ligand.scm If CCP4 is not available, let's get the monomer files from greg data dir. monomer-molecule-from-3-let-code still needs to provide a valid molecule for the test to pass. ------------------------------------------------------------------------ r956 | pemsley | 2008-04-09 12:40:16 +0100 (Wed, 09 Apr 2008) | 4 lines Changed paths: M /trunk/greg-tests/03-ligand.scm Change test to throw untested on invalid molecule, not lack of CCP4. Which makes "Get monomer test" pass if monomer-3GP.pdb and libcheck_3GP.cif exist in the current directory. ------------------------------------------------------------------------ r955 | pemsley | 2008-04-09 12:30:08 +0100 (Wed, 09 Apr 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Add graphics_info_t::use_graphics_interface_flag protection to set_model_toolbar_style(). ------------------------------------------------------------------------ r954 | pemsley | 2008-04-09 10:40:26 +0100 (Wed, 09 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm do better at getting a build result when the web page is not there. ------------------------------------------------------------------------ r953 | pemsley | 2008-04-09 09:07:09 +0100 (Wed, 09 Apr 2008) | 2 lines Changed paths: M /trunk/build-it Remove the test status file of this run, not a gtk2 one. ------------------------------------------------------------------------ r952 | pemsley | 2008-04-08 19:31:35 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/python-tests/Makefile.am Fix up the python tests, so that the source tar gets made correctly. ------------------------------------------------------------------------ r951 | pemsley | 2008-04-08 17:15:42 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it Update build-it placement of log files to match gtk2 version. ------------------------------------------------------------------------ r950 | pemsley | 2008-04-08 17:14:58 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix a typo in write-pdb. ------------------------------------------------------------------------ r949 | pemsley | 2008-04-08 14:20:13 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add protection in case the test status does not exist. ------------------------------------------------------------------------ r948 | pemsley | 2008-04-08 14:19:15 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update build test results. Better results from Ubuntu now? ------------------------------------------------------------------------ r947 | pemsley | 2008-04-08 14:05:48 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc use gtk_window_set_default_size() not gtk_window_resize() for gtk1. ------------------------------------------------------------------------ r946 | pemsley | 2008-04-08 13:42:48 +0100 (Tue, 08 Apr 2008) | 4 lines Changed paths: M /trunk/build-it M /trunk/build-web-page-builder.scm M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/restraints-editor/restraints-editor.glade M /trunk/restraints-editor/src/main.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-state.cc M /trunk/src/main.cc Change build-it to put logs in more standard place. More tinkering with web page builder, spacing reordering. Change graphics window/glarea size usage. [Ethan Merritt bug] ------------------------------------------------------------------------ r945 | b.lohkamp | 2008-04-07 19:13:00 +0100 (Mon, 07 Apr 2008) | 3 lines Changed paths: M /trunk/configure.in M /trunk/coot-gtk2.glade A /trunk/python-tests/Makefile.am M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c move smooth scroll preferences from maps to general put python-test into distribution ------------------------------------------------------------------------ r944 | pemsley | 2008-04-06 16:05:56 +0100 (Sun, 06 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm handle entities with a macro. ------------------------------------------------------------------------ r943 | b.lohkamp | 2008-04-05 21:38:05 +0100 (Sat, 05 Apr 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py toolbutton connection fix ------------------------------------------------------------------------ r942 | pemsley | 2008-04-05 20:20:30 +0100 (Sat, 05 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix the test pass text from the remote log. ------------------------------------------------------------------------ r941 | pemsley | 2008-04-05 12:32:34 +0100 (Sat, 05 Apr 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Add links to summary page. ------------------------------------------------------------------------ r940 | pemsley | 2008-04-05 12:07:43 +0100 (Sat, 05 Apr 2008) | 3 lines Changed paths: M /trunk/greg-tests/06-ssm.scm M /trunk/src/graphics-info-superpose.cc Fix superpose-with-atom-selection bug (hopefully). Added another test (new test data needed). ------------------------------------------------------------------------ r939 | pemsley | 2008-04-05 12:06:46 +0100 (Sat, 05 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc remove debugging. ------------------------------------------------------------------------ r938 | pemsley | 2008-04-04 17:32:50 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add build results from foreign build hosts. ------------------------------------------------------------------------ r937 | pemsley | 2008-04-04 17:28:15 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/group-settings.scm M /trunk/scheme/tips.scm Fix up typo in the setting of rapper-dir. ------------------------------------------------------------------------ r936 | pemsley | 2008-04-04 16:05:10 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Change test for guile-gtk ------------------------------------------------------------------------ r935 | pemsley | 2008-04-04 12:30:18 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm adjust the output files names. ------------------------------------------------------------------------ r934 | pemsley | 2008-04-04 12:22:36 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a bit of bolding. ------------------------------------------------------------------------ r933 | b.lohkamp | 2008-04-04 11:20:04 +0100 (Fri, 04 Apr 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/Makefile.am M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in A /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-state.cc M /trunk/src/gtk-manual.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/molecule-class-info.h added python toolbar buttons with 'manager' moved .coot*preferences.* to dir ~/.preferences/coot*preferences.* ------------------------------------------------------------------------ r932 | pemsley | 2008-04-04 11:10:48 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add status of last build. ------------------------------------------------------------------------ r931 | pemsley | 2008-04-04 10:35:40 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Write build/test status more consistently. ------------------------------------------------------------------------ r930 | pemsley | 2008-04-04 00:35:30 +0100 (Fri, 04 Apr 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple echo to a file the build and test status. To be picked up by the web page builder. ------------------------------------------------------------------------ r929 | pemsley | 2008-04-03 14:44:46 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/db-main/db-strands.cc Now that reference structures have strand info, we can use them. ------------------------------------------------------------------------ r928 | pemsley | 2008-04-03 14:44:03 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add chem_comp to dict_chem_comp constructor. ------------------------------------------------------------------------ r927 | pemsley | 2008-04-03 14:42:49 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix up the info about environment variables. ------------------------------------------------------------------------ r926 | pemsley | 2008-04-03 13:33:16 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Tabularise the results. ------------------------------------------------------------------------ r925 | pemsley | 2008-04-03 09:14:04 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a title. Add a link for the svn log. ------------------------------------------------------------------------ r924 | pemsley | 2008-04-02 16:47:56 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Copy over binary file to York if we are in biop. ------------------------------------------------------------------------ r923 | pemsley | 2008-04-02 16:46:47 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/group-settings.scm Trivial changes for rapper support. ------------------------------------------------------------------------ r922 | pemsley | 2008-04-02 16:46:02 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm More updates, now to handle build log links from outside York. ------------------------------------------------------------------------ r921 | pemsley | 2008-04-02 15:29:23 +0100 (Wed, 02 Apr 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh Add the operator<< for various classes. They had only been friends before. Reported by Morten. ------------------------------------------------------------------------ r920 | pemsley | 2008-04-02 15:12:48 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Add use_graphics_interface_flag around create_no_restraints_info_dialog(). ------------------------------------------------------------------------ r919 | pemsley | 2008-04-02 14:18:08 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add horne test for refinement with no graphics and no dictionary. ------------------------------------------------------------------------ r918 | pemsley | 2008-04-02 14:10:45 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Don't create dialogs about refinement when there is no graphics. ------------------------------------------------------------------------ r917 | pemsley | 2008-04-02 14:08:34 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Set up ccp4 on cycle in test. ------------------------------------------------------------------------ r916 | pemsley | 2008-04-02 14:08:03 +0100 (Wed, 02 Apr 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Take out Gtk2 build on FC2 for the moment (guile-gtk does not compile there). Add logs for ubuntu build. ------------------------------------------------------------------------ r915 | pemsley | 2008-04-02 14:06:59 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Change the name from NCS Loop to something more sensible. ------------------------------------------------------------------------ r914 | pemsley | 2008-04-02 14:06:20 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Correctly save the type of bond restraints (e.g. coval). ------------------------------------------------------------------------ r913 | pemsley | 2008-04-01 12:13:23 +0100 (Tue, 01 Apr 2008) | 2 lines Changed paths: M /trunk/greg-tests/07-ncs.scm Add NCS Residue Range copy test. ------------------------------------------------------------------------ r912 | pemsley | 2008-04-01 12:09:37 +0100 (Tue, 01 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Also redirect std err for building guile extras. ------------------------------------------------------------------------ r911 | pemsley | 2008-04-01 11:45:19 +0100 (Tue, 01 Apr 2008) | 7 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/support-gtk2-extras.c Fix range function in coot-utils. Use gtk_image_new_from_stock not gtk_image_new_from_icon_name for the clear icon in the toolbar (gtk 2.4, FC3). Change to InsResidue not AddResidue where we can for NCS residue range copy. #ifdef out each toolbar function. I was getting confused. Simplify test for guile-gtk. ------------------------------------------------------------------------ r910 | pemsley | 2008-03-31 14:18:32 +0100 (Mon, 31 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes update notes from impala. ------------------------------------------------------------------------ r909 | pemsley | 2008-03-31 10:46:10 +0100 (Mon, 31 Mar 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Put the tar file name into 16-coot.txt log Change text for svn revision output. ------------------------------------------------------------------------ r908 | pemsley | 2008-03-31 10:45:11 +0100 (Mon, 31 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix typo in logic of compiling conditional gtk_combo_box_get_active_text(). ------------------------------------------------------------------------ r907 | pemsley | 2008-03-31 10:31:50 +0100 (Mon, 31 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Find svn code revision. ------------------------------------------------------------------------ r906 | pemsley | 2008-03-30 21:31:09 +0100 (Sun, 30 Mar 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/dnotes Output the page generation time/date. Update notes. ------------------------------------------------------------------------ r905 | pemsley | 2008-03-30 21:29:09 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/coords/mmdb-crystal.h uncommented the include of Cartesian.h so that r899 compiles for Bill. Strange. ------------------------------------------------------------------------ r904 | pemsley | 2008-03-30 21:26:03 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.hh operator[] for atom ids should be/have been const. ------------------------------------------------------------------------ r903 | pemsley | 2008-03-30 19:07:03 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc #if tests for gtk version around gtk_combo_box_get_active_text(). ------------------------------------------------------------------------ r902 | pemsley | 2008-03-30 10:34:07 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a refresh of 10 minutes. ------------------------------------------------------------------------ r901 | pemsley | 2008-03-30 02:37:30 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add python fc3 version. ------------------------------------------------------------------------ r900 | pemsley | 2008-03-29 20:05:33 +0000 (Sat, 29 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm More build targets. ------------------------------------------------------------------------ r899 | pemsley | 2008-03-29 12:25:06 +0000 (Sat, 29 Mar 2008) | 3 lines Changed paths: M /trunk/atom-utils/Makefile.am Add -I $(top_srcdir)/ccp4mg-utils to INCLUDES so that atom-utils can fit mgtree.h from a clean install. ------------------------------------------------------------------------ r898 | pemsley | 2008-03-29 07:48:17 +0000 (Sat, 29 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm More sober colours. ------------------------------------------------------------------------ r897 | pemsley | 2008-03-28 22:07:36 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a limit to the bar size. ------------------------------------------------------------------------ r896 | pemsley | 2008-03-28 22:04:38 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Update web page builder to output coloured bars. ------------------------------------------------------------------------ r895 | pemsley | 2008-03-28 17:40:14 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Change the title. ------------------------------------------------------------------------ r894 | pemsley | 2008-03-28 16:12:43 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/sequence-view/Makefile.am Add ccp4mg-utils to INCLUDES for mgtree.h ------------------------------------------------------------------------ r893 | b.lohkamp | 2008-03-28 15:06:00 +0000 (Fri, 28 Mar 2008) | 1 line Changed paths: M /trunk/src/callbacks.c M /trunk/src/callbacks.h gtk1 fixes ------------------------------------------------------------------------ r892 | pemsley | 2008-03-28 12:35:47 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Fix error checking of maps (again). Now the function can actually read a map. ------------------------------------------------------------------------ r891 | pemsley | 2008-03-28 12:26:10 +0000 (Fri, 28 Mar 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-info.cc M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add torsion id to torsion restrain info. Fix addional representations and undo bug. ------------------------------------------------------------------------ r890 | pemsley | 2008-03-28 10:57:49 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: A /trunk/restraints-editor A /trunk/restraints-editor/restraints-editor.glade A /trunk/restraints-editor/src A /trunk/restraints-editor/src/Makefile.am A /trunk/restraints-editor/src/main.cc Add code for restraints editor - not in main app yep - just creating/storage/testing. ------------------------------------------------------------------------ r889 | b.lohkamp | 2008-03-28 10:57:35 +0000 (Fri, 28 Mar 2008) | 9 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-glue-gtk2.c A /trunk/src/coot-gtk2.defs M /trunk/src/coot-preferences.h M /trunk/src/coot_pythonmodule.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c add toolbar style to preferences removed the following from the menu (actually hidden for easy recovery): HID-> Virtual trackball Edit-> Font size & Pink Pointer size Draw-> Recentre, dragged map, smooth recentre & antialias added glue code (python and guile) for the toolbar changed toolbar items (Reset View etc) to toolbuttons Python function for adding toolbar buttons ------------------------------------------------------------------------ r888 | pemsley | 2008-03-26 15:52:15 +0000 (Wed, 26 Mar 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am gtk-manual.c to gtk-manual.cc in src/Makefile.am ------------------------------------------------------------------------ r887 | pemsley | 2008-03-26 15:36:37 +0000 (Wed, 26 Mar 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/02-shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc Fix valgrind-found bug in reading bogus map. Remove some debugging. Make the Mitch Miller test rotate less. ------------------------------------------------------------------------ r886 | b.lohkamp | 2008-03-26 15:20:31 +0000 (Wed, 26 Mar 2008) | 5 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/ncs.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-render.cc more python functions (ncs_ligand, ncs_ghost... and guis) some more unittest functions (not tested yet) 'fixed' zoom/angle for povray images (not perfect but reasonable) backwards building in loop fitting (was actually there already...) ------------------------------------------------------------------------ r885 | pemsley | 2008-03-26 14:26:06 +0000 (Wed, 26 Mar 2008) | 2 lines Changed paths: A /trunk/build-web-page-builder.scm (from /trunk/pe-test.scm:884) D /trunk/pe-test.scm Rename to build-web-page-builder.scm ------------------------------------------------------------------------ r884 | pemsley | 2008-03-26 14:24:53 +0000 (Wed, 26 Mar 2008) | 2 lines Changed paths: A /trunk/pe-test.scm web page builder added. Needs a name change. ------------------------------------------------------------------------ r883 | pemsley | 2008-03-25 14:10:23 +0000 (Tue, 25 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-python.cc Add string checking in key_sym_code_py(). ------------------------------------------------------------------------ r882 | pemsley | 2008-03-25 14:05:28 +0000 (Tue, 25 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-python.cc Add "coot-utils.hh" include for key sym decoding from python. ------------------------------------------------------------------------ r881 | pemsley | 2008-03-25 13:50:16 +0000 (Tue, 25 Mar 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/scheme/ncs.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-maps.cc Add NCS ligands function and GUI. Add inverse-rtop function (calling clipper function across scripting layer). transform-coord-molecule renamed transform-coords-molecule. set-molecule-name now updates the name in the Display Control Window. Add command line to rapper gui - needs testing. ------------------------------------------------------------------------ r880 | pemsley | 2008-03-24 21:48:44 +0000 (Mon, 24 Mar 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/ncs.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Changes so that we transform the screen centre on NCS jumping - no longer go to the related CA. Cuter, especially for ligands. ------------------------------------------------------------------------ r879 | pemsley | 2008-03-24 21:10:51 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r878 | pemsley | 2008-03-24 14:00:56 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/08-utils.scm M /trunk/ideal/lograma.h M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Export NCS ghost info to the scripting layer. ------------------------------------------------------------------------ r877 | pemsley | 2008-03-24 05:41:10 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: A /trunk/greg-tests/08-utils.scm M /trunk/greg-tests/Makefile.am M /trunk/greg-tests/begin.grg M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-scm.cc Add more testing for the key symms. ------------------------------------------------------------------------ r876 | pemsley | 2008-03-24 05:04:26 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-utils.hh A /trunk/coot-utils/gdk-keysym.awk A /trunk/coot-utils/gdk-keysyms.cc M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-scm.cc M /trunk/src/cc-interface.hh Add function to decode a string to a key index - for use in key bindings. ------------------------------------------------------------------------ r875 | pemsley | 2008-03-23 23:37:51 +0000 (Sun, 23 Mar 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm Fix up NCS maps test - 5 extra molecules. ------------------------------------------------------------------------ r874 | pemsley | 2008-03-23 12:36:44 +0000 (Sun, 23 Mar 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Fix typo in NCS map test. ------------------------------------------------------------------------ r873 | pemsley | 2008-03-22 23:07:34 +0000 (Sat, 22 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/snarf-coot-docs.scm Fix up water chain define for doc snarfing. ------------------------------------------------------------------------ r872 | pemsley | 2008-03-22 22:20:29 +0000 (Sat, 22 Mar 2008) | 6 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/ligand/test-ligand.cc M /trunk/ligand/torsion-general.cc M /trunk/ligand/torsion-general.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h The change_by() function of torsion_general now takes a tree pointer. (that is the initial tree on startup - so that the tree is not calculated and changed on every mouse motion - thus causing a bug). Utility get_first_res_of_moving_atoms() function added. ------------------------------------------------------------------------ r871 | pemsley | 2008-03-22 21:03:22 +0000 (Sat, 22 Mar 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-other.cc Document "Make a difference map". "Apply NCS loop..." function added to extensions. make-difference-map-gui added to coot-gui.scm Fixed lighting of display list objects. Works better now for me. Fixed colouring of Ball and Stick atoms. ------------------------------------------------------------------------ r870 | pemsley | 2008-03-22 18:13:13 +0000 (Sat, 22 Mar 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Cartesian.cc M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-state.cc M /trunk/src/gtk-manual.cc Adjust the picking algorithm, so that atoms at the back of the slab score worse. Make set_graphics_window_size() work properly. ------------------------------------------------------------------------ r869 | pemsley | 2008-03-22 17:02:10 +0000 (Sat, 22 Mar 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/graphics-info-pick.cc M /trunk/src/gtk-manual.cc Reorder header files so that gtk-manual.cc compiles on bubbles. ------------------------------------------------------------------------ r868 | pemsley | 2008-03-22 16:31:52 +0000 (Sat, 22 Mar 2008) | 4 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-state.cc M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.hh M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h More additional representation code. Now they are displayed in the Display Control dialog. And saved into the state file. ------------------------------------------------------------------------ r867 | pemsley | 2008-03-22 09:16:39 +0000 (Sat, 22 Mar 2008) | 8 lines Changed paths: M /trunk/TODO M /trunk/configure.in M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h D /trunk/src/gtk-manual.c A /trunk/src/gtk-manual.cc (from /trunk/src/gtk-manual.c:859) M /trunk/src/gtk-manual.h A /trunk/src/gtk-manual.hh M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Remove LINGUAS code from configure.in Add dynamically-tranformed map test. gtk-manual.c ->gtk-manual.cc Add gtk-manual.hh - for C++ interface. Add set_show_additional_representation(). Fix dynamically-tranformed map bug. Document set-default-temperature-factor-for-new-atoms ------------------------------------------------------------------------ r866 | b.lohkamp | 2008-03-15 16:25:10 +0000 (Sat, 15 Mar 2008) | 1 line Changed paths: M /trunk/src/graphics-info-render.cc fixed povray camera position (zoom still a bit out) ------------------------------------------------------------------------ r865 | b.lohkamp | 2008-03-14 20:10:57 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/python/povray.py M /trunk/python/raster3d.py M /trunk/scheme/hello.scm M /trunk/scheme/povray.scm M /trunk/scheme/raster3d.scm M /trunk/src/graphics-info-render.cc some povray fixes (sadly still not properly working... the camera position...) ------------------------------------------------------------------------ r864 | pemsley | 2008-03-14 13:00:15 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc Don't allow translation drag of intermediate atoms when they are a rotamer. ------------------------------------------------------------------------ r863 | pemsley | 2008-03-14 12:54:31 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/scheme/mutate.scm Fix typo error in delete-sidechain-range. ------------------------------------------------------------------------ r862 | pemsley | 2008-03-14 12:53:22 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes A template for additional representations. Not sure if I like it. ------------------------------------------------------------------------ r861 | pemsley | 2008-03-14 09:43:03 +0000 (Fri, 14 Mar 2008) | 3 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc Fix problem of not working ligand search when Flexible ligand is used with e.g. SO4. ------------------------------------------------------------------------ r860 | pemsley | 2008-03-13 19:32:54 +0000 (Thu, 13 Mar 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/src/c-interface-info.cc Sidestep bug coot_gui.py in handling string for history. In restraints code, use unsigned int where needed for cleanness. ------------------------------------------------------------------------ r859 | pemsley | 2008-03-13 17:37:59 +0000 (Thu, 13 Mar 2008) | 2 lines Changed paths: M /trunk/mapview.glade M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/interface.c Correct widget names in add_rep_dialog for gtk1. ------------------------------------------------------------------------ r858 | pemsley | 2008-03-13 16:36:51 +0000 (Thu, 13 Mar 2008) | 9 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/scheme/tips.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.c M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a scheme Missing Atoms gui to Extensions. Fill wrapped_create_add_additional_representation_gui(). And add_additional_representation_by_widget(). Works now except: ball and stick, needs to get bond width from combobox in gtk1. Add home on the range (a menu item) for additional representations. Skeleton alignment_results_scm() and alignment_results_py() added. ------------------------------------------------------------------------ r857 | pemsley | 2008-03-13 13:37:27 +0000 (Thu, 13 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot.in M /trunk/src/interface.c M /trunk/src/interface.h Add gtk1 add_reps_dialog. Make source. ------------------------------------------------------------------------ r856 | b.lohkamp | 2008-03-12 10:26:45 +0000 (Wed, 12 Mar 2008) | 4 lines Changed paths: M /trunk/build-it-win M /trunk/coords/Cartesian.cc M /trunk/coords/Cartesian.h M /trunk/coot-gtk2.glade M /trunk/cootrc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc changed size of gtk's icons in refinement toolbar (avoids elongated window) fixed docked accept_reject_dialog (key binding and crash when changing modes) some MinGW windows fixes ------------------------------------------------------------------------ r855 | pemsley | 2008-03-11 12:09:47 +0000 (Tue, 11 Mar 2008) | 2 lines Changed paths: A /trunk/scheme/a-rapper-gui.scm Add a Rapper GUI. ------------------------------------------------------------------------ r854 | pemsley | 2008-03-11 12:07:34 +0000 (Tue, 11 Mar 2008) | 3 lines Changed paths: M /trunk/src/coot.in Kludge in 1.8 to GUILE_LOAD_PATH - addresses Kevin's Ubuntu build/install problem? ------------------------------------------------------------------------ r853 | pemsley | 2008-03-10 11:09:15 +0000 (Mon, 10 Mar 2008) | 2 lines Changed paths: M /trunk/mapview.glade Add a gtk1 version of the additional representation dialog. ------------------------------------------------------------------------ r852 | pemsley | 2008-03-07 19:46:16 +0000 (Fri, 07 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix the typo in the python output of chem_comp_bond - spotted by Nigel M. ------------------------------------------------------------------------ r851 | pemsley | 2008-03-07 15:04:18 +0000 (Fri, 07 Mar 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade Name the widgets in add_reps_dialog. ------------------------------------------------------------------------ r850 | pemsley | 2008-03-07 14:18:13 +0000 (Fri, 07 Mar 2008) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm Change the key binding mechanism. Now we have add-key-binding function. Much cleaner. ------------------------------------------------------------------------ r849 | pemsley | 2008-03-07 12:54:13 +0000 (Fri, 07 Mar 2008) | 5 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Remove cruffty get_text_for_go_to_atom_chain_xxx() functions. Add bond width arg to additional_representation scripting functions. Fix up problems with creating/reading restraints in python scripting. It can eat its own dog food now, I think. ------------------------------------------------------------------------ r848 | pemsley | 2008-03-07 11:53:49 +0000 (Fri, 07 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Add use_graphics_interface protection in post_go_to_atom_window(). ------------------------------------------------------------------------ r847 | pemsley | 2008-03-07 01:41:15 +0000 (Fri, 07 Mar 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/gtk2-interface.c Use new style partial charge info. Add a Addition Representation gui to glade. Not used or properly filled. ------------------------------------------------------------------------ r846 | pemsley | 2008-03-07 00:01:29 +0000 (Fri, 07 Mar 2008) | 13 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/command-line.h Add function save-dialog-positions-to-init-file Add a hook for it in the extensions menu. Add a greg test case "Post Go To Atom no molecules". Rework the partial charge info in the dictionary. Now it carries a flag. This is how it will be for xyz positions too (i.e. pairs, one of which is a bool saying if this is a valid field or not). Add the reading of model coords into dictionary. Not finish yet. Or tested. Add function additional_representation_info_scm() Add command line option -c - but not activated yet - when shall the command line string be evaluated? Urgency hints removed from coot-gt2.glade. Hmm... ------------------------------------------------------------------------ r845 | pemsley | 2008-03-06 15:39:18 +0000 (Thu, 06 Mar 2008) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h More additional representation code. Now new bonds can be generated from the scripting layer. And cleared. We need a GUI. ------------------------------------------------------------------------ r844 | pemsley | 2008-03-06 12:24:13 +0000 (Thu, 06 Mar 2008) | 2 lines Changed paths: M /trunk/db-main/db-main.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/molecule-class-info.cc Add tweaks from Francois. ------------------------------------------------------------------------ r843 | b.lohkamp | 2008-03-06 09:26:36 +0000 (Thu, 06 Mar 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py fix coot_gui.py for use with coot commands in assignments ------------------------------------------------------------------------ r842 | pemsley | 2008-03-05 23:14:50 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: A /trunk/geometry/test-read-components.cc A /trunk/geometry/test-read-components.hh Add test-read-components files. ------------------------------------------------------------------------ r841 | pemsley | 2008-03-05 23:10:31 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc More pythonization of restraints code. ------------------------------------------------------------------------ r840 | pemsley | 2008-03-05 19:30:19 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/c-interface-info.cc Clean up pythonization of restraints interface. ------------------------------------------------------------------------ r839 | pemsley | 2008-03-05 18:54:46 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Continuing pythonization of restraints input/output. ------------------------------------------------------------------------ r838 | pemsley | 2008-03-05 18:53:04 +0000 (Wed, 05 Mar 2008) | 9 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/dnotes M /trunk/geometry/Makefile.am M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/ideal/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-navigation.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Rework the intelligent_goto_next/previous atom function. Now we can "next" over insertion codes and gaps. SCM goto_next_atom_maybe() function created for testing. atom_to_atom_index() function created to quickly get atom index. Add greg-test for this. Start on addition represenations: display_bonds() split to allow for addtional representations. Add the mitch miller test for NPD atoms from shelx files. ------------------------------------------------------------------------ r837 | pemsley | 2008-03-05 08:42:14 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c update splash screen. ------------------------------------------------------------------------ r836 | pemsley | 2008-03-05 08:40:52 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.5-pre.xpm Add a new splash screen ------------------------------------------------------------------------ r835 | pemsley | 2008-03-05 08:39:18 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/main.cc update the splash screen. ------------------------------------------------------------------------ r834 | b.lohkamp | 2008-03-04 15:11:45 +0000 (Tue, 04 Mar 2008) | 1 line Changed paths: M /trunk/build-it-win updated MinGW autobuild script ------------------------------------------------------------------------ r833 | pemsley | 2008-03-04 14:47:23 +0000 (Tue, 04 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix syntax errors of adding Refinement map protection to add_terminal_residue(). ------------------------------------------------------------------------ r832 | pemsley | 2008-03-04 08:34:32 +0000 (Tue, 04 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add refinement map test to add_terminal_residue() [like BL suggested]. ------------------------------------------------------------------------ r831 | pemsley | 2008-03-03 19:39:13 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/gtk2-interface.c More pythonization of restraints code. ------------------------------------------------------------------------ r830 | b.lohkamp | 2008-03-03 17:11:57 +0000 (Mon, 03 Mar 2008) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/povray.py M /trunk/python/raster3d.py M /trunk/python/shelx.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/04_cootaneer.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h python unittest functions complete and functional (as of today) added and fixed some python (scripting) functions ------------------------------------------------------------------------ r829 | pemsley | 2008-03-03 15:41:22 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/gl-matrix.cc M /trunk/src/gl-matrix.h Change the gl error handler, useful for NPD anisotropic atom matrices. ------------------------------------------------------------------------ r828 | pemsley | 2008-03-03 15:08:00 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-navigation-gtk2.cc Add protection for invalid go_to_atom_molecule. ------------------------------------------------------------------------ r827 | pemsley | 2008-03-03 13:56:20 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc A bit of Pythonization of restraints import/export code. ------------------------------------------------------------------------ r826 | b.lohkamp | 2008-03-01 22:37:19 +0000 (Sat, 01 Mar 2008) | 1 line Changed paths: A /trunk/build-it-win autobuild script for MinGW ------------------------------------------------------------------------ r825 | b.lohkamp | 2008-03-01 17:17:32 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/python/coot_utils.py D /trunk/python-tests/01-pdb+mtz.py A /trunk/python-tests/01_pdb_mtz.py A /trunk/python-tests/02_shelx.py D /trunk/python-tests/03-ligand.py A /trunk/python-tests/03_ligand.py A /trunk/python-tests/04_cootaneer.py A /trunk/python-tests/05_rna_ghosts.py A /trunk/python-tests/06_ssm.py A /trunk/python-tests/07_ncs.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_python.cc added more python unittest functions ------------------------------------------------------------------------ r824 | pemsley | 2008-03-01 13:05:07 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r823 | pemsley | 2008-03-01 13:03:37 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Improve error reporting. ------------------------------------------------------------------------ r822 | pemsley | 2008-03-01 13:02:49 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Handle EQIV card better. ------------------------------------------------------------------------ r821 | pemsley | 2008-03-01 13:02:12 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/autogen.sh Fix up code block spacing. ------------------------------------------------------------------------ r820 | pemsley | 2008-03-01 13:01:50 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/src/junk.cc Add mmcif reading code test case for Eugene, to junk.cc ------------------------------------------------------------------------ r819 | pemsley | 2008-02-29 11:04:35 +0000 (Fri, 29 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix problem of not running tests when build_coot_prerelease not set. ------------------------------------------------------------------------ r818 | pemsley | 2008-02-29 10:31:10 +0000 (Fri, 29 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Add guile-1.6.x fix ups ------------------------------------------------------------------------ r817 | pemsley | 2008-02-29 01:32:22 +0000 (Fri, 29 Feb 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh More monomer restraints parsing. Now we go both ways. ------------------------------------------------------------------------ r816 | pemsley | 2008-02-28 14:17:18 +0000 (Thu, 28 Feb 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.hh Add operator[] for plane restraints (needed for previous restraints using code). ------------------------------------------------------------------------ r815 | pemsley | 2008-02-28 14:06:50 +0000 (Thu, 28 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fill monomer_restraints() function. ------------------------------------------------------------------------ r814 | pemsley | 2008-02-28 12:45:21 +0000 (Thu, 28 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface.cc update notes, tidy formatting. ------------------------------------------------------------------------ r813 | pemsley | 2008-02-28 12:43:51 +0000 (Thu, 28 Feb 2008) | 3 lines Changed paths: M /trunk/src/graphics-info-superpose.cc Fix problem of fitting over wrong molecle, when using copy in superpose_with_atom_selection(). Fixes crash. ------------------------------------------------------------------------ r812 | pemsley | 2008-02-28 12:22:59 +0000 (Thu, 28 Feb 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm don't use run-gtk-pending-events, it is not defined when no graphics. ------------------------------------------------------------------------ r811 | pemsley | 2008-02-28 11:14:13 +0000 (Thu, 28 Feb 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Ooops. I'd forgotten to add fixed atom flags to chiral volume restraints. Fixes crash on bubbles - and errors elsewhere, I suspect. ------------------------------------------------------------------------ r810 | pemsley | 2008-02-27 14:18:08 +0000 (Wed, 27 Feb 2008) | 10 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc Move GTk functios from c-interface.cc into c-interface-gui.cc setup_python_window_entry() setup_guile_window_entry() python_window_enter_callback() guile_window_enter_callback() fill_option_menu_with_map_options() fill_option_menu_with_skeleton_options() set_contour_sigma_button_and_entry() set_contour_by_sigma_step_maybe() ------------------------------------------------------------------------ r809 | pemsley | 2008-02-27 14:12:34 +0000 (Wed, 27 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix up char * usage in PyRunSimpleString in python_window_enter_callback(). ------------------------------------------------------------------------ r808 | b.lohkamp | 2008-02-27 14:10:55 +0000 (Wed, 27 Feb 2008) | 1 line Changed paths: M /trunk/src/c-interface.cc fixed python scripting gtk version issue ------------------------------------------------------------------------ r807 | pemsley | 2008-02-27 12:59:30 +0000 (Wed, 27 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple If build_coot_prerelease by line 942, don't touch it or $run_tests. ------------------------------------------------------------------------ r806 | pemsley | 2008-02-27 12:49:32 +0000 (Wed, 27 Feb 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/06-ssm.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc Add a return value to try_assign_cell() in coot-shelx-ins.cc Remove some debugging. Add run-gtk-pending-events function. ------------------------------------------------------------------------ r805 | pemsley | 2008-02-27 11:37:02 +0000 (Wed, 27 Feb 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-shelx.hh M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Set the filled_flag for a ShelxIns in the constructor. Add some debugging. ------------------------------------------------------------------------ r804 | pemsley | 2008-02-27 11:34:53 +0000 (Wed, 27 Feb 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm Reorder tests. Allow a little wriggle room in 0 values from differnce map on a different grid. ------------------------------------------------------------------------ r803 | pemsley | 2008-02-27 09:33:19 +0000 (Wed, 27 Feb 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Fix isTer() test for closest_atom(). Fixes crash. ------------------------------------------------------------------------ r802 | b.lohkamp | 2008-02-26 23:17:09 +0000 (Tue, 26 Feb 2008) | 3 lines Changed paths: M /trunk/python/coot_utils.py A /trunk/python-tests A /trunk/python-tests/01-pdb+mtz.py A /trunk/python-tests/03-ligand.py A /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-mmdb.cc M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc some fixes for MINGW compilation add python-tests and some python unittest functions (more to come) ------------------------------------------------------------------------ r801 | pemsley | 2008-02-26 14:44:09 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: A /trunk/ideal/lograma.cpp A /trunk/ideal/lograma.h A /trunk/ideal/logramatest.cpp Add Kevin's LogRama class and test program ------------------------------------------------------------------------ r800 | pemsley | 2008-02-26 13:58:00 +0000 (Tue, 26 Feb 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/greg-tests/01-pdb+mtz.scm Add the alt conf residue deletion test - JED bug. Pretty up the report of the test result. ------------------------------------------------------------------------ r799 | pemsley | 2008-02-26 12:54:01 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple More adjustments to building guile-gtk ------------------------------------------------------------------------ r798 | pemsley | 2008-02-26 12:47:08 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix up guile_gtk build variable usage. ------------------------------------------------------------------------ r797 | pemsley | 2008-02-26 08:33:02 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-map.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc Commit for previous commit notes (was wrong dir). ------------------------------------------------------------------------ r796 | pemsley | 2008-02-26 08:28:05 +0000 (Tue, 26 Feb 2008) | 23 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/group-settings.scm M /trunk/scheme/snarf-coot-docs.scm Add another dummy function for snarfing. Add function first-n. Abstract interesting-residue-gui. Add commented mitch miller aniso test. Add "mask and difference map" greg test. Remove the commands to save the moving of the window from the history (too noisy). save_symmetry_coords_from_fileselection moved to c-interface-gui.cc quote arg of atom-info history. Same for save_coordinates(). Add function difference_map() and coot-map-utils code for that. install_map() renamed to install_ghost_map(). Check atom->isTer() for NCS differences and in atom button list returned to Go To Atom dialog. Added several debuggings. Reorder args to save_symmetry_coords() In molecule_info_class_t::delete_residue_with_altconf() check that an atoms are suitable for deletion before deleting the atom selection [JED]. Check for atom->isTer() in atom_pick(). Add Ramachandran restraints support in simple-restraints.cc/hh Add lograma class from Kevin (first "flat 0" version). Add args to with-map to test torsion and rama restraints. ------------------------------------------------------------------------ r795 | pemsley | 2008-02-26 07:52:23 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Try new guile-gtk build variables. ------------------------------------------------------------------------ r794 | b.lohkamp | 2008-02-18 19:53:43 +0000 (Mon, 18 Feb 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/tips.py M /trunk/scheme/tips.scm M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Fix automatic file sorting and filtering in gtk2 fileselection ------------------------------------------------------------------------ r793 | b.lohkamp | 2008-02-17 16:31:12 +0000 (Sun, 17 Feb 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c option to automatically set file filter for file chooser ------------------------------------------------------------------------ r792 | b.lohkamp | 2008-02-16 13:30:54 +0000 (Sat, 16 Feb 2008) | 1 line Changed paths: M /trunk/src/c-inner-main.c M /trunk/src/c-interface-preferences.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-preferences.cc M /trunk/src/main.cc fixes for gtk1 compilation ------------------------------------------------------------------------ r791 | b.lohkamp | 2008-02-15 20:31:32 +0000 (Fri, 15 Feb 2008) | 6 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/Makefile.am M /trunk/src/c-inner-main.c M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc A /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc implemented Preferences dialog (writes either or both, guile and python files) on the way added some extra bitmap glut atom label fonts, possibly obsolete menu items are not removed yet preferences are trumped by state files and .coot files python preferences are trumped by scm references ------------------------------------------------------------------------ r790 | pemsley | 2008-02-15 01:05:12 +0000 (Fri, 15 Feb 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add generic-object-name from scm function) ------------------------------------------------------------------------ r789 | pemsley | 2008-02-14 14:07:38 +0000 (Thu, 14 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/ncs.scm M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Fix occassional "flatlanding" when ncs chain skipping [JED]. ------------------------------------------------------------------------ r788 | pemsley | 2008-02-14 12:56:28 +0000 (Thu, 14 Feb 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h symm_colour changed to symmetry_colour and symmetry_colour_merge_weight is made a single variable, not an array. set symmetry colour and colour merge is added to the state file [fixes Doug Kuntz request]. ------------------------------------------------------------------------ r787 | pemsley | 2008-02-14 09:40:54 +0000 (Thu, 14 Feb 2008) | 5 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c add_ccp4i_projects_to_optionmenu() now takes the file_selection_type as an argument so that we can encode it in position passed to option_menu_refmac_ccp4i_project_signal_func(). Save python from the rsync filter. ------------------------------------------------------------------------ r786 | pemsley | 2008-02-13 16:56:51 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-build.cc remove extra erase_last_molecule() calls in new_molecule functions. ------------------------------------------------------------------------ r785 | pemsley | 2008-02-13 12:29:38 +0000 (Wed, 13 Feb 2008) | 5 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info-ncs.cc Fix up the NCS differences geometry graph. It should be more robust now. Add water_chain_from_shelx_ins to scripting layer. Add start of partial charges code. ------------------------------------------------------------------------ r784 | pemsley | 2008-02-13 12:25:34 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm Add shelx test and non-happy path tests. ------------------------------------------------------------------------ r783 | pemsley | 2008-02-13 12:24:15 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm Add functions for snarfing. ------------------------------------------------------------------------ r782 | pemsley | 2008-02-13 12:23:20 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/pixmaps/add-water.svg M /trunk/pixmaps/side-chain-180.svg Tinker with icons. ------------------------------------------------------------------------ r781 | pemsley | 2008-02-13 12:22:40 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/build-it Add Joseph Moran's CC fix. ------------------------------------------------------------------------ r780 | pemsley | 2008-02-13 09:04:54 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use --strip 1 for python patch, not -p0. ------------------------------------------------------------------------ r779 | pemsley | 2008-02-13 08:45:47 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add in cci patches when building Python (from Nigel Moriarty). ------------------------------------------------------------------------ r778 | pemsley | 2008-02-12 17:53:37 +0000 (Tue, 12 Feb 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info-ncs.cc ncs_residue_info_t is not to be used if filled is not 1. Fixes mad max residue number and problem creating graph x axis [JED]. ------------------------------------------------------------------------ r777 | pemsley | 2008-02-12 16:52:47 +0000 (Tue, 12 Feb 2008) | 4 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/positioned-widgets.h More work on fixed atom dialog. Now it behaves sensibly when an atom is picked - a wrapper for the dialog is used and stored as a static. ------------------------------------------------------------------------ r776 | pemsley | 2008-02-12 15:28:04 +0000 (Tue, 12 Feb 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade A /trunk/pixmaps/anchor.svg M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/support-gtk2-extras.c Add Fixed atom Toolbar icon. Add destroy callback to fixed atom dialog. ------------------------------------------------------------------------ r775 | pemsley | 2008-02-12 08:56:02 +0000 (Tue, 12 Feb 2008) | 4 lines Changed paths: M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh Remove GUILE_VERSION debugging from configure.in Change to toolbarbutton for fixed atoms in model_toolbar. Add fixup-gtk2-interface.sh for old gtk2 file choosers. ------------------------------------------------------------------------ r774 | pemsley | 2008-02-12 08:36:02 +0000 (Tue, 12 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add in the Neil Jerram guile-gui patch. ------------------------------------------------------------------------ r773 | pemsley | 2008-02-11 23:02:29 +0000 (Mon, 11 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove pycairo build and fix up test for build for guile_gtk ------------------------------------------------------------------------ r772 | pemsley | 2008-02-11 22:44:43 +0000 (Mon, 11 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple remove freetype etc dependencies of pycairo. ------------------------------------------------------------------------ r771 | pemsley | 2008-02-11 22:42:23 +0000 (Mon, 11 Feb 2008) | 2 lines Changed paths: M /trunk/src/coot.in set PYTHONHOME in coot, because of relocatability. ------------------------------------------------------------------------ r770 | pemsley | 2008-02-11 18:21:18 +0000 (Mon, 11 Feb 2008) | 3 lines Changed paths: M /trunk/configure.in D /trunk/src/coot A /trunk/src/coot.in (from /trunk/src/coot:769) configure.in sets GUILE_VERSION and that macro is exanded in coot.in to make coot, so that coot loads guile modules correctly. ------------------------------------------------------------------------ r769 | pemsley | 2008-02-11 18:10:59 +0000 (Mon, 11 Feb 2008) | 3 lines Changed paths: M /trunk/src/coot Add setting for GUILE_VERSION so that guile loads properly from coot with version 1.8 guile. ------------------------------------------------------------------------ r768 | b.lohkamp | 2008-02-11 10:14:03 +0000 (Mon, 11 Feb 2008) | 1 line Changed paths: M /trunk/src/c-interface-preferences.cc filled generic_object_name_py ------------------------------------------------------------------------ r767 | pemsley | 2008-02-10 21:34:33 +0000 (Sun, 10 Feb 2008) | 3 lines Changed paths: M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py Comment out pygtk.require("2.0") in coot_load_modules.py. Comment out sep.props.sensitive = False in extension.py. ------------------------------------------------------------------------ r766 | pemsley | 2008-02-10 03:11:10 +0000 (Sun, 10 Feb 2008) | 10 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/pixmaps/refine-1.svg M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h A /trunk/src/fixup-gtk2-interface.sh M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c In configure.in change to 2.4.12 for GTK version check. Add (GTK_MINOR_VERSION < 10) to gtk2_file_chooser_selector/chooser usage. Similarly #def out GtkFileChooserConfirmation usage in callbacks.c and callbacks.h Add fixup-gtk2-interface.sh to remove 2.8 dependencies. Currently we need to run this by hand. That should be automated later. Add fixed atom check in graphics-info-defines.cc Add pkg-config test for gtk in build-it-gtk-simple so that we can know if we need to fix up guile-gtk's gtk-glue.c ------------------------------------------------------------------------ r765 | pemsley | 2008-02-09 23:25:49 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface-preferences.cc Fix typo in iobj. ------------------------------------------------------------------------ r764 | pemsley | 2008-02-09 23:15:02 +0000 (Sat, 09 Feb 2008) | 3 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h Pass back a SCM for generic_object_name() and generic_object_index() checks for closed generic objects and ignore them. ------------------------------------------------------------------------ r763 | pemsley | 2008-02-09 15:48:45 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use pygtk 2.8.6 for simple build too. ------------------------------------------------------------------------ r762 | pemsley | 2008-02-09 15:46:53 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Us pygtk version 2.8.6 not 2.12.1, can we now build pygtk on FC5 machine? ------------------------------------------------------------------------ r761 | pemsley | 2008-02-09 11:15:35 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add back building of gtkglext. ------------------------------------------------------------------------ r760 | pemsley | 2008-02-09 00:13:57 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: A /trunk/build-it-gtk2-simple Remove gtk2 and pkg-config building. Test for Fedora core 5. ------------------------------------------------------------------------ r759 | pemsley | 2008-02-09 00:11:01 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix logic of atk installation. ------------------------------------------------------------------------ r758 | pemsley | 2008-02-08 19:27:50 +0000 (Fri, 08 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 gtk2 version testing. ------------------------------------------------------------------------ r757 | pemsley | 2008-02-08 18:28:03 +0000 (Fri, 08 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Try requiring gtk 2.10 ------------------------------------------------------------------------ r756 | pemsley | 2008-02-08 17:42:36 +0000 (Fri, 08 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 lib cleaning problems, add debugging. ------------------------------------------------------------------------ r755 | pemsley | 2008-02-07 14:59:14 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/pixmaps/rigid-body.svg M /trunk/pixmaps/side-chain-180.png M /trunk/pixmaps/side-chain-180.svg Update a couple of icons. ------------------------------------------------------------------------ r754 | pemsley | 2008-02-07 13:46:05 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Tinker with build_gmp logic. ------------------------------------------------------------------------ r753 | pemsley | 2008-02-07 13:44:15 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Add coot-preferences.h to Makefile.am ------------------------------------------------------------------------ r752 | pemsley | 2008-02-07 13:12:31 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Grr... Spell validation-graphs correctly. Sigh. ------------------------------------------------------------------------ r751 | pemsley | 2008-02-07 12:48:14 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Oops. Add validation-graphs.hh to the Makefile.am too. ------------------------------------------------------------------------ r750 | pemsley | 2008-02-07 12:41:21 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add test and build of ATK, needed for gtk+2.10.x ------------------------------------------------------------------------ r749 | pemsley | 2008-02-07 09:19:32 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/snarf-coot-docs.scm Fix ncs-chain-ids-scm for correct snarfing. ------------------------------------------------------------------------ r748 | pemsley | 2008-02-07 08:52:25 +0000 (Thu, 07 Feb 2008) | 6 lines Changed paths: M /trunk/atom-utils/Makefile.am M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/happy-coot-diary.html M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c The other major part of the molecule array -> vector changes. These are to move the validation graphs, the ramachandran plots and sequence view into the molecules. set_validation_graph() and get_validation_graph() functions created. erase_last_molecule()s have been matched to create_molecule()s. ------------------------------------------------------------------------ r747 | pemsley | 2008-02-06 19:09:40 +0000 (Wed, 06 Feb 2008) | 2 lines Changed paths: A /trunk/src/validation-graphs.hh Oops. Add validation-graphs header. ------------------------------------------------------------------------ r746 | b.lohkamp | 2008-02-06 18:10:11 +0000 (Wed, 06 Feb 2008) | 7 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/refmac.py M /trunk/src/Makefile.am D /trunk/src/add-coot-i-extern.sh M /trunk/src/coot.i M /trunk/src/coot.py D /trunk/src/coot_pre.i changed interesting_things_gui back to gtk.window (uses nested gtk mainloop now) changed coot.i back (apparently do not need any extern statements...) cosmetic changes to read_refmac_log ------------------------------------------------------------------------ r745 | pemsley | 2008-02-06 17:53:07 +0000 (Wed, 06 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info.h match create_molecules() with erase_last_molecule() in c-interface-build.cc ------------------------------------------------------------------------ r744 | pemsley | 2008-02-06 17:51:21 +0000 (Wed, 06 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 More tinkering with tests for pango, cairo etc. Change to the version Bernhard recommends. ------------------------------------------------------------------------ r743 | b.lohkamp | 2008-02-06 14:18:03 +0000 (Wed, 06 Feb 2008) | 6 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/refmac.py M /trunk/src/Makefile.am A /trunk/src/add-coot-i-extern.sh M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot M /trunk/src/coot.i A /trunk/src/coot_pre.i M /trunk/src/main.cc tooltip for interesting_things_gui (required change from gtk.window to gtk.dialog); used in read_refmac_log coot.i can be generated from coot_pre.i with src/add-coot-i-extern.sh (auto- matically adds extern to PyObjects from c-interface.h etc.). Remember to run when additional py functions are avaliable!! ------------------------------------------------------------------------ r742 | pemsley | 2008-02-04 11:37:43 +0000 (Mon, 04 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface.cc Add the ability to turn off DTI stereo (thanks Hartmut Luecke). ------------------------------------------------------------------------ r741 | b.lohkamp | 2008-02-02 16:18:41 +0000 (Sat, 02 Feb 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot A /trunk/src/coot-preferences.h M /trunk/src/coot.i M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c include COOT_PYTHON_DIR in coot some python functions tollbars and variable notebook tabs for preferences, add coot-preferences.h fixed python scripting window for non-pygtk (including memory issue) ------------------------------------------------------------------------ r740 | pemsley | 2008-02-01 14:18:05 +0000 (Fri, 01 Feb 2008) | 4 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.cc M /trunk/mapview.glade M /trunk/src/add-c-extern.sh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info-maps.cc Make tests pass - fix return value of handle-read-ccp4-map. Remove some debugging from simple-restraint.cc. Add fixed atom dialog - gtk1 version. ------------------------------------------------------------------------ r739 | pemsley | 2008-02-01 13:20:47 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Add fixed atom dialog. ------------------------------------------------------------------------ r738 | pemsley | 2008-02-01 13:10:01 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Remove "force redraw" debugging line. ------------------------------------------------------------------------ r737 | pemsley | 2008-02-01 13:05:14 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.h Fix up fixed atom in refinement. They work now (but from scripting, not gui) ------------------------------------------------------------------------ r736 | pemsley | 2008-02-01 02:36:26 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix up test for pygobject and pygtk. ------------------------------------------------------------------------ r735 | pemsley | 2008-02-01 02:29:06 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix problem in scripting args to coot's configure. ------------------------------------------------------------------------ r734 | pemsley | 2008-01-31 18:55:28 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/gtk2-interface.c further improvements on the fixed atoms in refinement. ------------------------------------------------------------------------ r733 | pemsley | 2008-01-31 15:37:19 +0000 (Thu, 31 Jan 2008) | 6 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/happy-coot-diary.html M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Changed fixed atom to be specs that are passed to simple_restraint. simple_restraint needs to properly handle the fixed atoms when generating the restraints. build-it-gtk2: Change HOSTLOGDIR to include gtk2 to separate it from gtk1 build logs. ------------------------------------------------------------------------ r732 | pemsley | 2008-01-31 14:00:26 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/coot.i M /trunk/src/junk.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Update code for fixing atoms. Not transfered to GUI or refinement code yet. ------------------------------------------------------------------------ r731 | pemsley | 2008-01-31 12:41:13 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc Move lots of molecule_class_info_t map functions to molecule-class-info-maps.cc. ------------------------------------------------------------------------ r730 | pemsley | 2008-01-31 08:40:26 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add extra tests for reading bogus mtz/maps. ------------------------------------------------------------------------ r729 | pemsley | 2008-01-31 08:39:26 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Make the log files be gtk2-build.log, to separate them out from gtk1 build. ------------------------------------------------------------------------ r728 | pemsley | 2008-01-30 17:23:23 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes rearrange cairo and librsvg. ------------------------------------------------------------------------ r727 | pemsley | 2008-01-30 16:26:51 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fontonfig added. ------------------------------------------------------------------------ r726 | pemsley | 2008-01-30 15:53:27 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Freetype2 building updates. ------------------------------------------------------------------------ r725 | pemsley | 2008-01-30 15:19:10 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Remove static patch (for sgi). Add test/build for freetype2 ------------------------------------------------------------------------ r724 | pemsley | 2008-01-30 09:36:48 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typo in pkg-configure build. ------------------------------------------------------------------------ r723 | pemsley | 2008-01-30 09:27:40 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typo in building of pkg-config. ------------------------------------------------------------------------ r722 | pemsley | 2008-01-30 09:25:54 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Add --pygtk to configure for coot. ------------------------------------------------------------------------ r721 | pemsley | 2008-01-30 02:54:51 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 librsvg depends on cairo apparently - reorder. ------------------------------------------------------------------------ r720 | pemsley | 2008-01-30 02:48:16 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix typo in gtk2 set test for failure. ------------------------------------------------------------------------ r719 | pemsley | 2008-01-30 02:40:03 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix pkg-config typo. ------------------------------------------------------------------------ r718 | pemsley | 2008-01-30 02:39:07 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix syntax error. ------------------------------------------------------------------------ r717 | pemsley | 2008-01-30 02:37:37 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 pycairo needs cairo 1.4.12 - so test for cairo, setting build_gtk=1 on failure. ------------------------------------------------------------------------ r716 | pemsley | 2008-01-30 00:34:11 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add test for pycairo ------------------------------------------------------------------------ r715 | pemsley | 2008-01-30 00:08:19 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Add pycairo. ------------------------------------------------------------------------ r714 | pemsley | 2008-01-29 18:56:06 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 pygobject typos. ------------------------------------------------------------------------ r713 | pemsley | 2008-01-29 18:52:34 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 more pygobject typos fixed. ------------------------------------------------------------------------ r712 | pemsley | 2008-01-29 18:49:47 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix typos. ------------------------------------------------------------------------ r711 | pemsley | 2008-01-29 18:46:31 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typos in build-it-gtk2 ------------------------------------------------------------------------ r710 | pemsley | 2008-01-29 18:37:59 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/greg-tests/Makefile.am Add ncs greg tests to tar file. ------------------------------------------------------------------------ r709 | pemsley | 2008-01-29 18:31:28 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Add pkg-config and pygobject builds. ------------------------------------------------------------------------ r708 | pemsley | 2008-01-29 16:30:56 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 M /trunk/src/c-interface-build.cc more debugging in the pygkt macro. ------------------------------------------------------------------------ r707 | b.lohkamp | 2008-01-29 16:20:54 +0000 (Tue, 29 Jan 2008) | 1 line Changed paths: M /trunk/python/extensions.py Fix Cootaneer-gui in extensions.py ------------------------------------------------------------------------ r706 | b.lohkamp | 2008-01-29 16:11:11 +0000 (Tue, 29 Jan 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/refmac.py refmac log file reader for python ------------------------------------------------------------------------ r705 | pemsley | 2008-01-29 15:44:23 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 M /trunk/src/c-interface-build.cc Remove ambiguity of double from python variable in constructing atom attributes. ------------------------------------------------------------------------ r704 | pemsley | 2008-01-29 15:22:02 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 pygtk settings, improved. ------------------------------------------------------------------------ r703 | pemsley | 2008-01-29 15:12:38 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Adjust pygtk settings so that it compiles in only if specified. ------------------------------------------------------------------------ r702 | pemsley | 2008-01-29 10:06:58 +0000 (Tue, 29 Jan 2008) | 4 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a SCM function refmac_params_scm(). Add function erase_last_molecule() for when we create a molecule, but fail to fill it. ------------------------------------------------------------------------ r701 | pemsley | 2008-01-28 19:46:54 +0000 (Mon, 28 Jan 2008) | 4 lines Changed paths: M /trunk/atom-utils/atom-utils.cc M /trunk/doc/Makefile.am M /trunk/doc/functions.tex M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/libtool M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/coot M /trunk/src/coot.py M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc Move from graphics::molecules begin an array to being a vector. Tests pass. Validation graphs need to be moved in to molecules. expand_molecule_space() needs some thought. ------------------------------------------------------------------------ r700 | pemsley | 2008-01-28 17:54:03 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add lib/python2.5 to the rsynced files. ------------------------------------------------------------------------ r699 | pemsley | 2008-01-28 17:45:18 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 more python debugging. ------------------------------------------------------------------------ r698 | pemsley | 2008-01-28 17:44:05 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Further python/pygtk tinkering. ------------------------------------------------------------------------ r697 | pemsley | 2008-01-28 17:30:46 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add a test for the existance of pygtk ------------------------------------------------------------------------ r696 | pemsley | 2008-01-28 16:57:04 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 add debugging/fixes. ------------------------------------------------------------------------ r695 | pemsley | 2008-01-28 16:54:13 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 add debugging. ------------------------------------------------------------------------ r694 | pemsley | 2008-01-28 16:50:33 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 add debugging. ------------------------------------------------------------------------ r693 | pemsley | 2008-01-26 15:44:29 +0000 (Sat, 26 Jan 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python/coot_load_modules.py.in M /trunk/scheme/mutate.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-mutate.cc Fix GTK Warning on using CCP4i option menu in a map file selector. Add test for atom order after mutation. Change order of arguments to mutate function. ------------------------------------------------------------------------ r692 | pemsley | 2008-01-25 23:35:02 +0000 (Fri, 25 Jan 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2 M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes Fix up write_ins_file_internal to return a good status on correct write. So that test passes. ------------------------------------------------------------------------ r691 | pemsley | 2008-01-25 23:14:56 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/07-ncs.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h A better name for NCS chains. Update greg test. ------------------------------------------------------------------------ r690 | pemsley | 2008-01-25 18:08:47 +0000 (Fri, 25 Jan 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Update the pepflip test, now that we have changed the arguments to the scripting function. ------------------------------------------------------------------------ r689 | pemsley | 2008-01-25 16:40:20 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm extra error messages from shelx greg test. ------------------------------------------------------------------------ r688 | pemsley | 2008-01-25 14:45:00 +0000 (Fri, 25 Jan 2008) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm Need to define scm commands in snarf-coot-docs.scm so that coot-utils.scm can be loaded OK. ------------------------------------------------------------------------ r687 | pemsley | 2008-01-25 14:13:31 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix refmac arg construction when using python. Should fix Bill Scott's bug. ------------------------------------------------------------------------ r686 | pemsley | 2008-01-25 12:44:27 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/macros/net-http-goosh.m4 Fix up macro test for guile-gui so that it doesn't try to use $DISPLAY. ------------------------------------------------------------------------ r685 | pemsley | 2008-01-25 11:50:49 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/train-pepflip.cc Update pepflip code. ------------------------------------------------------------------------ r684 | pemsley | 2008-01-25 00:45:35 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc Fill validation graph for NCS differences. ------------------------------------------------------------------------ r683 | pemsley | 2008-01-24 20:52:57 +0000 (Thu, 24 Jan 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-graphs.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h Add NCS differences to Validation menu on the GUI. Fix up (on penelope) accession button problems. ------------------------------------------------------------------------ r682 | pemsley | 2008-01-24 18:45:32 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 build-it-gtk extra notes. ------------------------------------------------------------------------ r681 | b.lohkamp | 2008-01-24 17:21:16 +0000 (Thu, 24 Jan 2008) | 7 lines Changed paths: M /trunk/configure.in M /trunk/macros/with-guile.m4 M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ncs.cc A /trunk/src/c-interface-python.cc A /trunk/src/c-interface-python.hh M /trunk/src/c-interface.h M /trunk/src/coot.i M /trunk/src/graphics-info.cc M /trunk/src/main.cc docked accept/reject toolbar shows distorsion chi2 as tooltip and extra information for chiral outliers (in the Chirals box) and introduced CIS petides (extra box). new python functions and file (c-interface-python.cc) configure with no --with-guile (or with --without-guile) ignores all guile configuring ------------------------------------------------------------------------ r680 | pemsley | 2008-01-24 12:55:43 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Further work on the NCS differences graph. ------------------------------------------------------------------------ r679 | pemsley | 2008-01-24 12:06:43 +0000 (Thu, 24 Jan 2008) | 3 lines Changed paths: M /trunk/src/gtk-manual.c M /trunk/src/gtk-manual.h M /trunk/src/molecule-class-info.cc Use GINT_TO_POINTER and GPOINTER_TO_INT not casting int * for display control window control. ------------------------------------------------------------------------ r678 | pemsley | 2008-01-24 01:01:22 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 gtk2 adjustments. ------------------------------------------------------------------------ r677 | pemsley | 2008-01-24 00:56:22 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 gtk2 adjustments. ------------------------------------------------------------------------ r676 | pemsley | 2008-01-24 00:51:43 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Gtk2 adjustments. ------------------------------------------------------------------------ r675 | pemsley | 2008-01-24 00:49:58 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Adjust build-it-gtk2, gtk2 dependencies. ------------------------------------------------------------------------ r674 | pemsley | 2008-01-24 00:45:03 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Build GTK2 from scratch: librsvg, cairo, pango, glitz. glib, gtk+-2 ------------------------------------------------------------------------ r673 | pemsley | 2008-01-23 14:07:36 +0000 (Wed, 23 Jan 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/train-pepflip.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ideal/pepflip.cc M /trunk/python/extensions.py M /trunk/scheme/coot-gui.scm M /trunk/scheme/fitting.scm M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc Add pepfip-active-residue. Add test-for-pepflip code into db-main. Trying to find a good metrix now. Eigen value filtering of fragments to speed things up. ------------------------------------------------------------------------ r672 | pemsley | 2008-01-23 09:30:00 +0000 (Wed, 23 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typo in guile test. ------------------------------------------------------------------------ r671 | pemsley | 2008-01-23 09:25:37 +0000 (Wed, 23 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Change the tests for gtk, and try to build guile with optimization. ------------------------------------------------------------------------ r670 | pemsley | 2008-01-22 18:29:48 +0000 (Tue, 22 Jan 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/dnotes M /trunk/greg-tests/02-shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Add a test for INS file from PDB. Make refinement button label configurable. If cell not found, add a cell from a mmdb manager in shelx writer. ------------------------------------------------------------------------ r669 | pemsley | 2008-01-22 18:26:53 +0000 (Tue, 22 Jan 2008) | 2 lines Changed paths: M /trunk/configure.in A /trunk/macros/net-http-goosh.m4 Test for net http, goosh and gui if guile is to be used. ------------------------------------------------------------------------ r668 | pemsley | 2008-01-22 14:48:32 +0000 (Tue, 22 Jan 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh Add a button to the accession code window. ------------------------------------------------------------------------ r667 | pemsley | 2008-01-22 12:35:59 +0000 (Tue, 22 Jan 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c Fix typo in GTK version test. ------------------------------------------------------------------------ r666 | b.lohkamp | 2008-01-22 11:28:36 +0000 (Tue, 22 Jan 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-int