The Coot Reference Manual
1. Acknowledgments
Paul Emsley is grateful to use the library code of the
following people, without whom Coot could not have been realised:
- Kevin Cowtan
- Eugene Krissinel
- Stuart McNicholas
- Raghavendra Chandrashekara
- Paul Bourke & Cory Gene Bloyd
For dictionaries:
- Alexei Vagin for Refmac Monomer Library
- Roland Dunbrack & co-workers for rotamer library data
Also (for generally useful software used in Coot):
- Matteo Frigo & Steven G. Johnson
- Gary Houston & other Guile developers
- Python developers
- GTk+ and GNOME-Canvas developers
- GNU Scientific Library developers
- OpenGL developers
- Janne Löf
Also those with whom Paul has corresponded or provided features and bug
fixes and built the software from source code:
- William G. Scott
- Bernhard Lohkamp
- Joel Bard
- Ezra Peisach
- Alex Schuettelkopf
- Charlie Bond
- Ethan Merritt
Not forgetting the testers(1)
- Eleanor J. Dodson
- Jan Dohnalek
- Karen McLuskey
- Bernhard Lohkamp
- Aleks Roszak
- Florence Vincent
- Roberto Steiner
- Alex Schuettelkopf
- Charlie Bond
- Constantina Fotinou
- Miguel Ortiz Lombardía
- William G. Scott
- Adrian Lapthorn
- Frank von Delft
Those with experience of Quanta, XFit and O will notice similarities
between Coot and those programs, it's fair to say that they have had
considerable influence in the look of Coot, so Paul respectively thanks
for inspiration: Tom Oldfield, Alwyn Jones (2) and Duncan McRee (and their co-workers).
2. Design Overview
2.1 Why?
"Why does Coot exist?" you might ask. "Given that other molecular
graphics (3) programs exist, why write
another?"
Because I like having the source code to programs I use and think/would
like/hope that others feel the same. Because the other programs don't
quite work how I wanted them to (4). Because there was the possibility to seamlessly
integrate molecular graphics into the CCP4 Suite/CCP4i and because there
was an opportunity to use new powerful CCP4 library code for
model-building.
As to why write Coot when CCP4MG was available: that is not how it
happened. Coot (5) was
released over a year before CCP4MG was available. I followed my own
design, GUI, toolkit and aesthetic decisions - for good or bad
(6).
2.2 Hacker's Guide
The are several core libraries that are fundamental to Coot:
- Clipper: Kevin Cowtan's General crystallographic object library
- mmdb: CCP4's Coordinate Library
- GTk+: GNU's GUI toolkit.
2.2.1 GUI
The GUI is almost entirely built using glade. Glade writes out its
code in pure C. This causes a problem. `src/interface.h' and
`src/support.h' both get regenerated in "C mode" every time
glade is run. So, after every time we change the GUI with glade, we
need to run `post-glade' to introduce the C/C++ linking type
declaration wrapper into these files.
Not all of the GUI is build with glade - there are dynamic elements,
for example the "Map and Molecule (Display) Control" window the
frame of which are generated in glade, but the hboxs are filled using
hand-made code (see `gtk-manual.c').
2.2.2 GUI/State Variables
The `graphics_info_t' class contains a host of static state
variables, mostly manipulated by GUI element (e.g button)
callbacks (7). For historical reasons they are initially set
in `globjects.cc'. Because the callbacks are written in C by
glade (8), these variables need a functional
interface to set the variables, and that interface is used by both the
GUI button (9) callbacks and is exported
to the scripting level. These function declarations are in
`c-interface.h'. All manipulations of `graphics_info_t''s
state variables go via `c-interface.h'.
Notice that MMDB functions are not allowed in
this interface (10).
2.2.3 Scripting
So, SWIG uses `c-interface.h' to generate the python/scheme
scripting interface. The scripting language is chosen at
configure-time using either --with-guile or
--with-python.
2.3 Validation
As I write this, a few of us are cobbling together a XML-based system
for validation. We think that validation data should be presented as
XML data that can be passed between packages and programs. Either the
program itself will output the data, or we will write a wrapper to
turn the output into the appropriate XML format.
These XML data will be then available for use in the molecular
graphics and will provide information for a "Next Unusual Feature"
button. The library to provide the XML cabability for this is expat,
the same library used in Perl's XML::Parser, Python's XML parser
Pyexpat and Mozilla's XML parser.
2.3.1 Example: Temperature Factor Analysis
Recall that the kurtosis of a distribution, k is given by:
We calculate the kurtosis for the isotropic temperature factors for
each residue in the molecule and residues with the most leptokurtic
distributions are written out to a file. The format of the file is
XML.
This is an example of how we expect validation data to be presented to
molecular graphics programs.
3. Exported Functions
So, here for reference purposes is the full list of user-accessable
functions exported to the scripting interface. I have tried to remove
from this list functions that pass or return a GtkWidget *, since
they are not useful in the scripting interface at the moment.
I hope to enable direct access to the menu-bar and menu items will be
available to the scripting layer at some stage in the future. This will
open the door to user-defined menus and (I hope) encourage 3rd-party
coot scripts.
3.0.1 (try-load-scheme-extras-dir)
3.1 File System Functions
3.1.1 (make-directory-maybe dir)
where:
3.1.2 (set-show-paths-in-display-manager i)
where:
- i is an exact integer number
3.1.3 (show-paths-in-display-manager-state)
3.1.4 (add-coordinates-glob-extension ext)
where:
3.1.5 (add-data-glob-extension ext)
where:
3.1.6 (add-dictionary-glob-extension ext)
where:
3.1.7 (add-map-glob-extension ext)
where:
3.1.8 (set-sticky-sort-by-date)
3.1.9 (set-filter-fileselection-filenames istate)
where:
- istate is an exact integer number
3.1.10 (filter-fileselection-filenames-state)
3.1.11 (set-file-chooser-selector istate)
where:
- istate is an exact integer number
3.1.12 (file-chooser-selector-state)
3.1.13 (set-file-chooser-overwrite istate)
where:
- istate is an exact integer number
3.1.14 (file-chooser-overwrite-state)
3.2 Widget Utilities
3.2.1 (info-dialog txt)
where:
3.3 Widget Utilities
3.3.1 (manage-column-selector filename)
where:
3.4 Molecule Info Functions
3.4.1 (chain-n-residues chain-id imol)
where:
- chain-id is a string
- imol is an exact integer number
3.4.2 (molecule-centre-internal imol iaxis)
where:
- imol is an exact integer number
- iaxis is an exact integer number
3.4.3 (n-chains imol)
where:
- imol is an exact integer number
3.4.4 (is-solvent-chain-p imol chain-id)
where:
- imol is an exact integer number
- chain-id is a string
3.4.5 (copy-molecule imol)
where:
- imol is an exact integer number
3.4.6 (exchange-chain-ids-for-seg-ids imol)
where:
- imol is an exact integer number
3.5 Library and Utility Functions
3.5.1 (set-molecule-name imol new-name)
where:
- imol is an exact integer number
- new-name is a string
3.5.2 (coot-real-exit retval)
where:
- retval is an exact integer number
3.5.3 (coot-clear-backup-or-real-exit retval)
where:
- retval is an exact integer number
3.5.4 (run-clear-backups retval)
where:
- retval is an exact integer number
3.5.5 (first-coords-imol)
3.6 Graphics Utility Functions
3.6.1 (set-do-anti-aliasing state)
where:
- state is an exact integer number
3.6.2 (do-anti-aliasing-state)
3.6.3 (set-do-GL-lighting state)
where:
- state is an exact integer number
3.6.4 (do-GL-lighting-state)
3.6.5 (use-graphics-interface-state)
3.6.6 (start-graphics-interface)
3.6.7 (reset-view)
3.6.8 (graphics-n-molecules)
3.6.9 (next-map-for-molecule imol)
where:
- imol is an exact integer number
3.6.10 (toggle-idle-spin-function)
3.6.11 (set-idle-function-rotate-angle f)
where:
3.6.12 (idle-function-rotate-angle)
3.6.13 (handle-read-draw-molecule filename)
where:
3.6.14 (read-pdb filename)
where:
3.6.15 (replace-fragment imol-target imol-fragment atom-selection)
where:
- imol-target is an exact integer number
- imol-fragment is an exact integer number
- atom-selection is a string
3.6.16 (screendump-image filename)
where:
3.7 Interface Preferences
3.7.1 (set-scroll-by-wheel-mouse istate)
where:
- istate is an exact integer number
3.7.2 (scroll-by-wheel-mouse-state)
3.7.3 (set-default-initial-contour-level-for-map n-sigma)
where:
- n-sigma is an inexact number
3.7.4 (set-default-initial-contour-level-for-difference-map n-sigma)
where:
- n-sigma is an inexact number
3.7.5 (print-view-matrix)
3.7.6 (get-view-matrix-element row col)
where:
- row is an exact integer number
- col is an exact integer number
3.7.7 (get-view-quaternion-internal element)
where:
- element is an exact integer number
3.7.8 (set-view-quaternion i j k l)
where:
- i is an inexact number
- j is an inexact number
- k is an inexact number
- l is an inexact number
3.7.9 (apply-ncs-to-view-orientation imol current-chain next-ncs-chain)
where:
- imol is an exact integer number
- current-chain is a string
- next-ncs-chain is a string
3.7.10 (set-fps-flag t)
where:
- t is an exact integer number
3.7.11 (get-fps-flag)
3.7.12 (set-show-origin-marker istate)
where:
- istate is an exact integer number
3.7.13 (show-origin-marker-state)
3.7.14 (suck-model-fit-dialog)
3.7.15 (suck-model-fit-dialog-bl)
3.7.16 (add-status-bar-text s)
where:
3.7.17 (set-model-fit-refine-dialog-stays-on-top istate)
where:
- istate is an exact integer number
3.7.18 (model-fit-refine-dialog-stays-on-top-state)
3.7.19 (set-accept-reject-dialog-docked state)
where:
- state is an exact integer number
3.7.20 (accept-reject-dialog-docked-state)
3.8 Mouse Buttons
3.8.1 (quanta-buttons)
3.8.2 (quanta-like-zoom)
3.8.3 (set-control-key-for-rotate state)
where:
- state is an exact integer number
3.8.4 (control-key-for-rotate-state)
3.8.5 (blob-under-pointer-to-screen-centre)
3.9 Cursor Function
3.9.1 (normal-cursor)
3.9.2 (fleur-cursor)
3.9.3 (pick-cursor-maybe)
3.9.4 (rotate-cursor)
3.9.5 (set-pick-cursor-index icursor-index)
where:
- icursor-index is an exact integer number
3.10 Model/Fit/Refine Functions
3.10.1 (post-model-fit-refine-dialog)
3.10.2 (unset-model-fit-refine-dialog)
3.10.3 (unset-refine-params-dialog)
3.10.4 (show-select-map-dialog)
3.10.5 (set-model-fit-refine-rotate-translate-zone-label txt)
where:
3.10.6 (set-model-fit-refine-place-atom-at-pointer-label txt)
where:
3.10.7 (unset-other-modelling-tools-dialog)
3.10.8 (post-other-modelling-tools-dialog)
3.11 Backup Functions
3.11.1 (make-backup imol)
where:
- imol is an exact integer number
3.11.2 (turn-off-backup imol)
where:
- imol is an exact integer number
3.11.3 (turn-on-backup imol)
where:
- imol is an exact integer number
3.11.4 (backup-state imol)
where:
- imol is an exact integer number
3.11.5 (apply-undo)
3.11.6 (apply-redo)
3.11.7 (set-have-unsaved-changes imol)
where:
- imol is an exact integer number
3.11.8 (have-unsaved-changes-p imol)
where:
- imol is an exact integer number
3.11.9 (set-undo-molecule imol)
where:
- imol is an exact integer number
3.11.10 (show-set-undo-molecule-chooser)
3.11.11 (show-set-undo-molecule-chooser-py)
3.11.12 (set-unpathed-backup-file-names state)
where:
- state is an exact integer number
3.11.13 (unpathed-backup-file-names-state)
3.12 Recover Session Function
3.12.1 (recover-session)
3.13 Map Functions
3.13.1 (calc-phases-generic mtz-file-name)
where:
- mtz-file-name is a string
3.13.2 (scroll-wheel-map)
3.13.3 (save-previous-map-colour imol)
where:
- imol is an exact integer number
3.13.4 (restore-previous-map-colour imol)
where:
- imol is an exact integer number
3.13.5 (set-active-map-drag-flag t)
where:
- t is an exact integer number
3.13.6 (get-active-map-drag-flag)
3.13.7 (set-last-map-colour f1 f2 f3)
where:
- f1 is an unknown type
- f2 is an unknown type
- f3 is an unknown type
3.13.8 (set-map-colour imol red green blue)
where:
- imol is an exact integer number
- red is an inexact number
- green is an inexact number
- blue is an inexact number
3.13.9 ( map-no gdouble[4])
where:
- map-no is an exact integer number
- gdouble[4] is an unknown type
3.13.10 (handle-symmetry-colour-change mol gdouble[4])
where:
- mol is an exact integer number
- gdouble[4] is an unknown type
3.13.11 (set-contour-level-absolute imol-map level)
where:
- imol-map is an exact integer number
- level is an inexact number
3.13.12 (set-contour-level-in-sigma imol-map level)
where:
- imol-map is an exact integer number
- level is an inexact number
3.13.13 (set-last-map-sigma-step f)
where:
3.13.14 (set-contour-by-sigma-step-by-mol f state imol)
where:
- f is an inexact number
- state is an exact integer number
- imol is an exact integer number
3.13.15 (data-resolution imol)
where:
- imol is an exact integer number
3.13.16 (solid-surface imap on-off-flag)
where:
- imap is an exact integer number
- on-off-flag is an exact integer number
3.13.17 (export-map imol filename)
where:
- imol is an exact integer number
- filename is a string
3.13.18 (rotate-map-round-screen-axis-x r-degrees)
where:
- r-degrees is an inexact number
3.13.19 (rotate-map-round-screen-axis-y r-degrees)
where:
- r-degrees is an inexact number
3.13.20 (rotate-map-round-screen-axis-z r-degrees)
where:
- r-degrees is an inexact number
3.14 Density Increment
3.14.1 (set-iso-level-increment val)
where:
3.14.2 (set-iso-level-increment-from-text text imol)
where:
- text is a string
- imol is an exact integer number
3.14.3 (set-diff-map-iso-level-increment val)
where:
3.14.4 (set-diff-map-iso-level-increment-from-text text imol)
where:
- text is a string
- imol is an exact integer number
3.14.5 (set-map-sampling-rate-text text)
where:
3.14.6 (set-map-sampling-rate r)
where:
3.14.7 (get-map-sampling-rate)
3.14.8 (set-scrollable-map imol)
where:
- imol is an exact integer number
3.14.9 (change-contour-level is-increment)
where:
- is-increment is an exact integer number
3.14.10 (set-last-map-contour-level level)
where:
- level is an inexact number
3.14.11 (set-last-map-contour-level-by-sigma n-sigma)
where:
- n-sigma is an inexact number
3.14.12 (set-stop-scroll-diff-map i)
where:
- i is an exact integer number
3.14.13 (set-stop-scroll-iso-map i)
where:
- i is an exact integer number
3.14.14 (set-stop-scroll-iso-map-level f)
where:
3.14.15 (set-stop-scroll-diff-map-level f)
where:
3.14.16 (set-residue-density-fit-scale-factor f)
where:
3.15 Density Functions
3.15.1 (set-map-line-width w)
where:
- w is an exact integer number
3.15.2 (map-line-width-state)
3.15.3 (mtz-file-has-phases-p mtz-file-name)
where:
- mtz-file-name is a string
3.15.4 (is-mtz-file-p filename)
where:
3.15.5 (auto-read-make-and-draw-maps filename)
where:
3.15.6 (set-auto-read-do-difference-map-too i)
where:
- i is an exact integer number
3.15.7 (auto-read-do-difference-map-too-state)
3.15.8 (set-density-size-from-widget text)
where:
3.15.9 (set-map-radius f)
where:
3.15.10 (set-density-size f)
where:
3.15.11 (set-map-radius-slider-max f)
where:
3.15.12 (set-display-intro-string str)
where:
3.15.13 (set-esoteric-depth-cue istate)
where:
- istate is an exact integer number
3.15.14 (esoteric-depth-cue-state)
3.15.15 (set-swap-difference-map-colours i)
where:
- i is an exact integer number
3.15.16 (set-map-is-difference-map imol)
where:
- imol is an exact integer number
3.15.17 (map-is-difference-map imol)
where:
- imol is an exact integer number
3.15.18 (another-level)
3.15.19 (another-level-from-map-molecule-number imap)
where:
- imap is an exact integer number
3.15.20 (residue-density-fit-scale-factor)
3.15.21 (density-at-point imol x y z)
where:
- imol is an exact integer number
- x is an inexact number
- y is an inexact number
- z is an inexact number
3.16 Parameters from map
3.16.1 (mtz-use-weight-for-map imol-map)
where:
- imol-map is an exact integer number
3.17 PDB Functions
3.17.1 (write-pdb-file imol file-name)
where:
- imol is an exact integer number
- file-name is a string
3.18 Refmac Functions
3.18.1 (set-refmac-molecule imol)
where:
- imol is an exact integer number
3.18.2 (set-refmac-counter imol refmac-count)
where:
- imol is an exact integer number
- refmac-count is an exact integer number
3.18.3 (swap-map-colours imol1 imol2)
where:
- imol1 is an exact integer number
- imol2 is an exact integer number
3.18.4 (set-keep-map-colour-after-refmac istate)
where:
- istate is an exact integer number
3.18.5 (keep-map-colour-after-refmac-state)
3.19 Symmetry Functions
3.19.1 (set-symmetry-size-from-widget text)
where:
3.19.2 (set-symmetry-size f)
where:
3.19.3 (get-show-symmetry)
3.19.4 (set-show-symmetry-master state)
where:
- state is an exact integer number
3.19.5 (set-show-symmetry-molecule mol-no state)
where:
- mol-no is an exact integer number
- state is an exact integer number
3.19.6 (symmetry-as-calphas mol-no state)
where:
- mol-no is an exact integer number
- state is an exact integer number
3.19.7 (get-symmetry-as-calphas-state imol)
where:
- imol is an exact integer number
3.19.8 (set-symmetry-molecule-rotate-colour-map imol state)
where:
- imol is an exact integer number
- state is an exact integer number
3.19.9 (symmetry-molecule-rotate-colour-map-state imol)
where:
- imol is an exact integer number
3.19.10 (set-symmetry-colour-by-symop imol state)
where:
- imol is an exact integer number
- state is an exact integer number
3.19.11 (set-symmetry-whole-chain imol state)
where:
- imol is an exact integer number
- state is an exact integer number
3.19.12 (set-symmetry-atom-labels-expanded state)
where:
- state is an exact integer number
3.19.13 (has-unit-cell-state imol)
where:
- imol is an exact integer number
3.19.14 (setup-save-symmetry-coords)
3.19.15 (set-space-group imol spg)
where:
- imol is an exact integer number
- spg is a string
3.19.16 (set-symmetry-shift-search-size shift)
where:
- shift is an exact integer number
3.20 File Selection Functions
3.20.1 (clear-refmac-ccp4i-project)
3.21 History Functions
3.21.1 (print-all-history-in-scheme)
3.21.2 (print-all-history-in-python)
3.21.3 (set-console-display-commands-state istate)
where:
- istate is an exact integer number
3.21.4 (set-console-display-commands-hilights bold-flag colour-flag colour-index)
where:
- bold-flag is an exact integer number
- colour-flag is an exact integer number
- colour-index is an exact integer number
3.21.5 (save-state)
3.21.6 (save-state-file filename)
where:
3.21.7 (set-save-state-file-name filename)
where:
3.21.8 (set-run-state-file-status istat)
where:
- istat is an exact integer number
3.21.9 (run-state-file)
3.21.10 (run-state-file-py)
3.21.11 (run-state-file-maybe)
3.21.12 (vt-surface mode)
where:
- mode is an exact integer number
3.21.13 (vt-surface-status)
3.22 Clipping Functions
3.22.1 (do-clipping1-activate)
3.22.2 (set-clipping-back v)
where:
3.22.3 (set-clipping-front v)
where:
3.23 Unit Cell
3.23.1 (get-show-unit-cell imol)
where:
- imol is an exact integer number
3.23.2 (set-show-unit-cells-all istate)
where:
- istate is an exact integer number
3.23.3 (set-show-unit-cell imol istate)
where:
- imol is an exact integer number
- istate is an exact integer number
3.23.4 (set-unit-cell-colour red green blue)
where:
- red is an inexact number
- green is an inexact number
- blue is an inexact number
3.24 Colour
3.24.1 (set-symmetry-colour-merge mol-no v)
where:
- mol-no is an exact integer number
- v is an inexact number
3.24.2 (set-colour-map-rotation-on-read-pdb f)
where:
3.24.3 (set-colour-map-rotation-on-read-pdb-flag i)
where:
- i is an exact integer number
3.24.4 (set-colour-map-rotation-on-read-pdb-c-only-flag i)
where:
- i is an exact integer number
3.24.5 (set-colour-by-chain imol)
where:
- imol is an exact integer number
3.24.6 (set-colour-by-molecule imol)
where:
- imol is an exact integer number
3.24.7 (set-colour-map-rotation-for-map f)
where:
3.24.8 (set-molecule-bonds-colour-map-rotation imol theta)
where:
- imol is an exact integer number
- theta is an inexact number
3.24.9 (get-molecule-bonds-colour-map-rotation imol)
where:
- imol is an exact integer number
3.25 Anisotropic Atoms
3.25.1 (get-limit-aniso)
3.25.2 (get-show-limit-aniso)
3.25.3 (get-show-aniso)
3.25.4 (set-limit-aniso state)
where:
- state is an exact integer number
3.25.5 (set-aniso-limit-size-from-widget text)
where:
3.25.6 (set-show-aniso state)
where:
- state is an exact integer number
3.25.7 (set-aniso-probability f)
where:
3.25.8 (get-aniso-probability)
3.26 Display Functions
3.26.1 (set-graphics-window-size x-size y-size)
where:
- x-size is an exact integer number
- y-size is an exact integer number
3.26.2 (set-graphics-window-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.3 (store-graphics-window-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.4 (graphics-draw)
3.26.5 (hardware-stereo-mode)
3.26.6 (stereo-mode-state)
3.26.7 (mono-mode)
3.26.8 (side-by-side-stereo-mode use-wall-eye-mode)
where:
- use-wall-eye-mode is an exact integer number
3.26.9 (set-hardware-stereo-angle-factor f)
where:
3.26.10 (hardware-stereo-angle-factor-state)
3.26.11 (set-model-fit-refine-dialog-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.12 (set-display-control-dialog-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.13 (set-go-to-atom-window-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.14 (set-delete-dialog-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.15 (set-rotate-translate-dialog-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.16 (set-accept-reject-dialog-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.26.17 (set-ramachandran-plot-dialog-position x-pos y-pos)
where:
- x-pos is an exact integer number
- y-pos is an exact integer number
3.27 Smooth Scrolling
3.27.1 (set-smooth-scroll-flag v)
where:
- v is an exact integer number
3.27.2 (get-smooth-scroll)
3.27.3 (set-smooth-scroll-steps-str t)
where:
3.27.4 (set-smooth-scroll-steps i)
where:
- i is an exact integer number
3.27.5 (set-smooth-scroll-limit-str t)
where:
3.27.6 (set-smooth-scroll-limit lim)
where:
3.28 Font Size
3.28.1 (set-font-size i)
where:
- i is an exact integer number
3.28.2 (get-font-size)
3.28.3 (set-font-colour red green blue)
where:
- red is an inexact number
- green is an inexact number
- blue is an inexact number
3.29 Rotation Centre
3.29.1 (set-rotation-centre-size-from-widget text)
where:
3.29.2 (set-rotation-centre-size f)
where:
3.29.3 (recentre-on-read-pdb)
3.29.4 (set-recentre-on-read-pdb int)
where:
- int is an exact integer number
3.29.5 (set-rotation-centre x y z)
where:
- x is an inexact number
- y is an inexact number
- z is an inexact number
3.29.6 (set-rotation-centre-internal x y z)
where:
- x is an inexact number
- y is an inexact number
- z is an inexact number
3.29.7 (rotation-centre-position axis)
where:
- axis is an exact integer number
3.30 Orthogonal Axes
3.30.1 (set-draw-axes i)
where:
- i is an exact integer number
3.31 Atom Selection Utilities
3.31.1 (atom-index imol chain-id iresno atom-id)
where:
- imol is an exact integer number
- chain-id is a string
- iresno is an exact integer number
- atom-id is a string
3.31.2 (median-temperature-factor imol)
where:
- imol is an exact integer number
3.31.3 (average-temperature-factor imol)
where:
- imol is an exact integer number
3.31.4 (clear-pending-picks)
3.31.5 (set-default-temperature-factor-for-new-atoms new-b)
where:
- new-b is an inexact number
3.31.6 (default-new-atoms-b-factor)
3.31.7 (set-atom-attribute imol chain-id resno ins-code atom-name alt-conf attribute-name val)
where:
- imol is an exact integer number
- chain-id is a string
- resno is an exact integer number
- ins-code is a string
- atom-name is a string
- alt-conf is an unknown type
- attribute-name is a string
- val is an inexact number
3.31.8 (set-atom-string-attribute imol chain-id resno ins-code atom-name alt-conf attribute-name attribute-value)
where:
- imol is an exact integer number
- chain-id is a string
- resno is an exact integer number
- ins-code is a string
- atom-name is a string
- alt-conf is an unknown type
- attribute-name is a string
- attribute-value is a string
3.31.9 (set-atom-attributes attribute-expression-list)
where:
- attribute-expression-list is an unknown type
3.31.10 (set-atom-attributes-py attribute-expression-list)
where:
- attribute-expression-list is an unknown type
3.32 Skeletonization
3.32.1 (skel-greer-on)
3.32.2 (skel-greer-off)
3.32.3 (skel-foadi-on)
3.32.4 (skel-foadi-off)
3.32.5 (skeletonize-map prune-flag imol)
where:
- prune-flag is an exact integer number
- imol is an exact integer number
3.32.6 (unskeletonize-map imol)
where:
- imol is an exact integer number
3.32.7 (set-initial-map-for-skeletonize)
3.32.8 (set-max-skeleton-search-depth v)
where:
- v is an exact integer number
3.32.9 (set-skeletonization-level-from-widget txt)
where:
3.32.10 (set-skeleton-box-size-from-widget txt)
where:
3.32.11 (set-skeleton-box-size f)
where:
3.33 Skeleton Colour
3.33.1 (handle-skeleton-colour-change mol map-col)
where:
- mol is an exact integer number
- map-col is an unknown type
3.33.2 (set-skeleton-colour imol r g b)
where:
- imol is an exact integer number
- r is an inexact number
- g is an inexact number
- b is an inexact number
3.34 Read CCP4 Map
3.34.1 (handle-read-ccp4-map filename is-diff-map-flag)
where:
- filename is an unknown type
- is-diff-map-flag is an exact integer number
3.35 Save Coordinates
3.35.1 (save-coordinates imol filename)
where:
- imol is an exact integer number
- filename is a string
3.35.2 (set-save-coordinates-in-original-directory i)
where:
- i is an exact integer number
3.35.3 (save-molecule-number-from-option-menu)
3.35.4 (set-save-molecule-number imol)
where:
- imol is an exact integer number
3.36 Read Phases File Functions
3.36.1 (possible-cell-symm-for-phs-file)
3.37 Graphics Move
3.37.1 (undo-last-move)
3.37.2 (translate-molecule-by imol x y z)
where:
- imol is an exact integer number
- x is an inexact number
- y is an inexact number
- z is an inexact number
3.38 Go To Atom Widget Functions
3.38.1 (post-go-to-atom-window)
3.38.2 (go-to-atom-molecule-number)
3.38.3 (go-to-atom-residue-number)
3.38.4 (set-go-to-atom-chain-residue-atom-name-no-redraw t1 iresno t3)
where:
- t1 is a string
- iresno is an exact integer number
- t3 is a string
3.38.5 (update-go-to-atom-from-current-position)
3.38.6 (atom-spec-to-atom-index mol chain resno atom-name)
where:
- mol is an exact integer number
- chain is a string
- resno is an exact integer number
- atom-name is a string
3.38.7 (update-go-to-atom-window-on-changed-mol imol)
where:
- imol is an exact integer number
3.38.8 (update-go-to-atom-window-on-new-mol)
3.38.9 (update-go-to-atom-window-on-other-molecule-chosen imol)
where:
- imol is an exact integer number
3.38.10 (set-go-to-atom-molecule imol)
where:
- imol is an exact integer number
3.38.11 (unset-go-to-atom-widget)
3.39 AutoBuilding functions (Defunct)
3.39.1 (autobuild-ca-off)
3.39.2 (test-fragment)
3.39.3 (do-skeleton-prune)
3.39.4 (test-function i j)
where:
- i is an exact integer number
- j is an exact integer number
3.40 Map and Molecule Control
3.40.1 (post-display-control-window)
3.40.2 (add-map-display-control-widgets)
3.40.3 (add-mol-display-control-widgets)
3.40.4 (add-map-and-mol-display-control-widgets)
3.40.5 (reset-graphics-display-control-window)
3.40.6 (close-graphics-display-control-window)
3.40.7 (set-map-displayed imol state)
where:
- imol is an exact integer number
- state is an exact integer number
3.40.8 (set-mol-displayed imol state)
where:
- imol is an exact integer number
- state is an exact integer number
3.40.9 (set-mol-active imol state)
where:
- imol is an exact integer number
- state is an exact integer number
3.40.10 (mol-is-displayed imol)
where:
- imol is an exact integer number
3.40.11 (mol-is-active imol)
where:
- imol is an exact integer number
3.40.12 (map-is-displayed imol)
where:
- imol is an exact integer number
3.40.13 (set-all-maps-displayed on-or-off)
where:
- on-or-off is an exact integer number
3.40.14 (set-all-models-displayed-and-active on-or-off)
where:
- on-or-off is an exact integer number
3.41 Merge Molecules
3.41.1 (do-merge-molecules-gui)
3.42 Mutate Sequence and Loops GUI
3.43 Align and Mutate
3.43.1 (align-and-mutate imol chain-id fasta-maybe)
where:
- imol is an exact integer number
- chain-id is a string
- fasta-maybe is a string
3.44 Renumber Residue Range
3.44.1 (change-residue-number imol chain-id current-resno current-inscode new-resno new-inscode)
where:
- imol is an exact integer number
- chain-id is a string
- current-resno is an exact integer number
- current-inscode is a string
- new-resno is an exact integer number
- new-inscode is a string
3.45 Change Chain ID
3.46 Scripting
3.46.1 (post-scripting-window)
3.46.2 (post-scheme-scripting-window)
3.46.3 (post-python-scripting-window)
3.46.4 (run-command-line-scripts)
3.46.5 (set-guile-gui-loaded-flag)
3.46.6 (set-python-gui-loaded-flag)
3.46.7 (set-found-coot-gui)
3.46.8 (get-monomer three-letter-code)
where:
- three-letter-code is a string
3.46.9 ( filename)
where:
3.46.10 ( filename)
where:
3.46.11 (run-python-script filename)
where:
3.47 Regularization and Refinement
3.47.1 (do-regularize state)
where:
- state is an exact integer number
3.47.2 (do-refine state)
where:
- state is an exact integer number
3.47.3 (add-planar-peptide-restraints)
3.47.4 (remove-planar-peptide-restraints)
3.47.5 (add-omega-torsion-restriants)
3.47.6 (remove-omega-torsion-restriants)
3.47.7 (set-refinement-immediate-replacement istate)
where:
- istate is an exact integer number
3.47.8 (refinement-immediate-replacement-state)
3.47.9 (set-residue-selection-flash-frames-number i)
where:
- i is an exact integer number
3.47.10 (accept-regularizement)
3.47.11 (clear-up-moving-atoms)
3.47.12 (clear-moving-atoms-object)
3.47.13 (do-peptide-torsions-toggle)
3.47.14 (set-refine-with-torsion-restraints istate)
where:
- istate is an exact integer number
3.47.15 (set-refine-params-phi-psi-restraints-type restraints-type)
where:
- restraints-type is an exact integer number
3.47.16 (set-matrix f)
where:
3.47.17 (matrix-state)
3.47.18 (set-refine-auto-range-step i)
where:
- i is an exact integer number
3.47.19 (set-refine-max-residues n)
where:
- n is an exact integer number
3.47.20 (refine-zone-atom-index-define imol ind1 ind2)
where:
- imol is an exact integer number
- ind1 is an exact integer number
- ind2 is an exact integer number