[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[ccp4bb]: Image production: in detail

To: "ccp4bb@dl.ac.uk" <ccp4bb@dl.ac.uk>
Subject: [ccp4bb]: Image production: in detail
From: Yong TANG <tang@moon.ibp.ac.cn>
Date: Tue, 19 Jun 2001 23:7:39 +0800
CC: "ccp4bb-owner@dl.ac.uk" <ccp4bb-owner@dl.ac.uk>
Organization: Institute of Biophysics
Reply-To: tang@moon.ibp.ac.cn
Sender: owner-ccp4bb@dl.ac.uk
***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Dear all,

Thanks for those who have responded to my problem. Before I could report a summary about this issue here. I wish I could have a chance to go into some specific details about my problems.

GRASP: Grasp would produce nice .ps files. However, for purpose of further processing, such as for labeling charged residues, I have to outport it from SGI to Adobe Photoshop in PC. Since I don't know any img-format (from .ps to .tiff, for example) conversion programs in SGI, I have to use 'snapshot'. Suggestions of using gimp or imagemagick for format conversion have led us to download the programs. But the installation of gimp failed. It complained that 'the gtk-config script installed by GTK could not be found', although we've installed the glib-1.2.8.tar.gz (obtained from www.GTK.org) before hand. I attached the log file at the end of this mail and wish somebody could help me out with this. Imagemagick seems to need more other things.

Stereo-pair electron density map superimposed with structure model: O is exhaustedly used for model building, but for image production Turbo-Frodo seems to achieve more brilliant color and much better ball-and-stick model, and is able to produce stereo pairs (although they will crossover at the middle). Sometimes the feature of Van der Vaals surface presentation in Turbo could be a simple reason why using it. In such case, snapshot seems to be the only way of catching the images. I've been advised to use Bobscript and am lucky enough to obtain it from Dr. Esnouf today (I wish it will help soon). But still, is there any other program producing good VDW surface images? 

Program Molscript and Raster3D have been running on our SGIs. Stereo-pairs production by Raster3d needs tiff library. However, we have real trouble in installing the tiff library. This make the production of stereo pairs with Raster3d impossible. We're using SGI O2 (Irix 6.5 operating system). We've downloaded the tiff software from www.libtiff.org (file: http://www.libtiff.org/tiff-v3.5.6-beta.tar.gz), but failed in compilation (there seems to be many errors, as attached below). Have I got the right thing, please?

It seems that if these two problem could be solved, I would be able to find my way out.

Best wishes,
Sincerely Yours,

Yong TANG
A doctorate student at:
Division of Structural Biology
National Lab of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences
15# Datun Road, Chaoyang District
Beijing 100101, P.R. China
Tel: 0086-10-64888511
E-mail: tang@moon.ibp.ac.cn	


++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++ Problem with gimp++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++

1). glib-1.2.8.tar.gz is from www.GTK.org and I've installed glib OK.
O21:/usr/local 64% find ./ -name '*glib*' -print
.../bin/glib-config
.../lib/libglib-1.2.so.1.8
.../lib/glib
.../lib/glib/include/glibconfig.h
.../lib/libglib.a
.../lib/libglib-1.2.so.1
.../lib/libglib-1.2.so
.../lib/libglib.so
.../lib/libglib.la
.../man/man1/glib-config.1
.../info/glib.info
.../share/aclocal/glib.m4
.../include/glib.h

2). gimp-1.2.1.tar.gz is from www.gimp.org
At configuration:
O21:/usr/people/tangy/bin/gimp-1.2.1 147% ./configure
creating cache ./config.cache
checking for a BSD compatible install... ./install-sh -c
checking whether build environment is sane... yes
checking whether make sets ${MAKE}... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for working makeinfo... missing
checking host system type... mips-sgi-irix6.5
checking build system type... mips-sgi-irix6.5
checking for ranlib... :
checking for gcc... no
checking for cc... cc
checking whether the C compiler (cc  ) works... yes
checking whether the C compiler (cc  ) is a cross-compiler... no
checking whether we are using GNU C... no
checking whether cc accepts -g... yes
checking for non-GNU ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
updating cache ./config.cache
loading cache ./config.cache within ltconfig
checking whether we are using GNU C... no
checking for object suffix... o
checking for executable suffix... no
checking for cc option to produce PIC... none
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.lo... yes
checking if cc static flag -non_shared works... none
checking if the linker (/usr/bin/ld -n32) is GNU ld... no
checking whether the linker (/usr/bin/ld -n32) supports shared libraries... yes
checking command to parse /usr/bin/nm -B output... ok
checking how to hardcode library paths into programs... immediate
checking for /usr/bin/ld -n32 option to reload object files... -r
checking dynamic linker characteristics... irix6.5 ld.so
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for objdir... .libs
creating libtool
updating cache ./config.cache
loading cache ./config.cache
checking whether to enable maintainer-specific portions of Makefiles... no
checking host system type... mips-sgi-irix6.5
checking for gcc... (cached) cc
checking whether the C compiler (cc -g ) works... yes
checking whether the C compiler (cc -g ) is a cross-compiler... no
checking whether we are using GNU C... (cached) no
checking whether cc accepts -g... (cached) yes
checking for POSIXized ISC... no
checking for cc option to accept ANSI C... none needed
checking for a BSD compatible install... ./install-sh -c
checking whether ln -s works... (cached) yes
checking whether make sets ${MAKE}... (cached) yes
checking how to run the C preprocessor... cc -E
checking for ANSI C header files... yes
checking for working const... yes
checking for inline... __inline
checking for off_t... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for unistd.h... yes
checking for getpagesize... yes
checking for working mmap... no
checking for argz.h... no
checking for limits.h... yes
checking for locale.h... yes
checking for nl_types.h... yes
checking for malloc.h... yes
checking for string.h... yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getcwd... yes
checking for munmap... yes
checking for putenv... yes
checking for setenv... no
checking for setlocale... yes
checking for strchr... yes
checking for strcasecmp... yes
checking for strdup... yes
checking for __argz_count... no
checking for __argz_stringify... no
checking for __argz_next... no
checking for stpcpy... no
checking for LC_MESSAGES... yes
checking whether NLS is requested... yes
checking whether included gettext is requested... no
checking for libintl.h... no
checking whether catgets can be used... no
checking for msgfmt... msgfmt
checking for gmsgfmt... msgfmt
checking for xgettext... :
checking for catalogs to be installed...  ca cs da de en_GB es fi fr ga gl hu hr it ja ko nl no pl pt_BR ru sk sv uk
checking for gtk-config... no
checking for GTK - version >= 1.2.8... no
*** The gtk-config script installed by GTK could not be found
*** If GTK was installed in PREFIX, make sure PREFIX/bin is in
*** your path, or set the GTK_CONFIG environment variable to the
*** full path to gtk-config.
configure: error: Test for GTK failed. See the file 'INSTALL' for help.

++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++++++ Problem with tiff library:++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++

O21:/usr/people/tangy/bin/tiff-v3.5.6-beta 77%  configure
Configuring TIFF Software v3.5.6
If configure does the wrong thing, check the file config.log for
information that may help you understand what went wrong.
Reading site-wide parameters from ./config.site.
Wow, you've got a mips-sgi-irix6.5 system!
Using /usr/bin/cc for a C compiler (use -with-CC=compilername to override).
Using -ansi to get the appropriate compilation environment.
Looks like /usr/bin/cc supports the -g option.
Using "-g" for C compiler options.
Using /sbin/make to configure the software.
Warning, no ranlib, assuming it's not needed.
Looks like ar has an s option to build symbol tables.
Using previously created libtiff/port.h.
Checking system libraries for functionality to emulate.
Done checking system libraries.
Checking for Dynamic Shared Object (DSO) support.
Looks like your system supports IRIX-style DSOs.
Done checking for DSO support.
Looks like there is support for SGI RGB images.
Looks like there is support for IRIS GL.
Selecting programs used during installation.
Looks like mv supports the -f option to force a move.
Looks like /sbin/ln supports the -s option to create a symbolic link.
Done selecting programs.
Selecting default TIFF configuration parameters.
Looks like manual pages go in /usr/local/man.
Looks like manual pages should be installed with sysv-nroff-compress-Z.
TIFF configuration parameters are:
[ 1] Directory for tools:               /usr/local/bin
[ 2] Directory for libraries:           /usr/local/lib
[ 3] Directory for include files:       /usr/local/include
[ 4] Directory for manual pages:        /usr/local/man
[ 5] Directory for HTML documents:      /usr/local/doc/libtiff
[ 6] Manual page installation scheme:   sysv-nroff-compress-Z
Are these ok [yes]? y
Creating Makefile from ./Makefile.in
Creating libtiff/Makefile from ./libtiff/Makefile.in
Creating man/Makefile from ./man/Makefile.in
Creating tools/Makefile from ./tools/Makefile.in
Creating port/install.sh from ./port/install.sh.in
Done.

O21:/usr/people/tangy/bin/tiff-v3.5.6-beta 78% make
--- all ---
= libtiff
--- all ---
        if [ IRIXdso != nodso ]; then  smake IRIXdso;  else  true;  fi
`IRIXdso' is up to date.
= tools
--- all ---
`sgi2tiff' is up to date.
`tiffgt' is up to date.
`tiffsv' is up to date.
= man
--- lib/Makefile ---
        test -d lib || mkdir lib
--- apps/Makefile ---
        test -d apps || mkdir apps
        smake apps/fax2tiff.1  apps/fax2ps.1  apps/gif2tiff.1  apps/pal2rgb.1  apps/ppm2tiff.1  apps/ras2tiff.1  apps/rgb2ycbcr.1  app
s/sgi2tiff.1  apps/thumbnail.1  apps/tiff2bw.1  apps/tiff2ps.1  apps/tiffcmp.1  apps/tiffcp.1  apps/tiffdither.1  apps/tiffdump.1  app
s/tiffgt.1  apps/tiffinfo.1  apps/tiffmedian.1  apps/tiffsplit.1  apps/tiffsv.1  
--- lib/Makefile ---
        smake lib/libtiff.3t   lib/TIFFClose.3t  lib/TIFFError.3t  lib/TIFFFlush.3t  lib/TIFFGetField.3t  lib/TIFFOpen.3t  lib/TIFFPri
ntDirectory.3t  lib/TIFFReadDirectory.3t  lib/TIFFReadEncodedStrip.3t  lib/TIFFReadEncodedTile.3t  lib/TIFFReadRGBAImage.3t  lib/TIFFR
eadRGBAStrip.3t  lib/TIFFReadRGBATile.3t  lib/TIFFReadRawStrip.3t  lib/TIFFReadRawTile.3t  lib/TIFFReadScanline.3t  lib/TIFFReadTile.3
t  lib/TIFFRGBAImage.3t  lib/TIFFSetDirectory.3t  lib/TIFFSetField.3t  lib/TIFFWarning.3t  lib/TIFFWriteDirectory.3t  lib/TIFFWriteEnc
odedStrip.3t  lib/TIFFWriteEncodedTile.3t  lib/TIFFWriteTile.3t  lib/TIFFWriteRawStrip.3t  lib/TIFFWriteRawTile.3t  lib/TIFFWriteScanl
ine.3t   lib/TIFFbuffer.3t  lib/TIFFcodec.3t  lib/TIFFmemory.3t  lib/TIFFquery.3t  lib/TIFFsize.3t  lib/TIFFstrip.3t  lib/TIFFswab.3t 
 lib/TIFFtile.3t   lib/TIFFmalloc.3t  lib/TIFFrealloc.3t  lib/TIFFfree.3t  lib/TIFFmemset.3t  lib/TIFFmemcpy.3t  lib/TIFFmemcmp.3t  li
b/TIFFComputeTile.3t  lib/TIFFCheckTile.3t  lib/TIFFNumberOfTiles.3t  lib/TIFFComputeStrip.3t  lib/TIFFNumberOfStrips.3t  lib/TIFFCurr
entDirectory.3t  lib/TIFFCurrentRow.3t  lib/TIFFCurrentStrip.3t  lib/TIFFCurrentTile.3t  lib/TIFFFdOpen.3t  lib/TIFFFileName.3t  lib/T
IFFFileno.3t  lib/TIFFFindCODEC.3t  lib/TIFFFlushData.3t  lib/TIFFGetMode.3t  lib/TIFFIsTiled.3t  lib/TIFFIsByteSwapped.3t  lib/TIFFIs
UpSampled.3t  lib/TIFFIsMSB2LSB.3t  lib/TIFFLastDirectory.3t  lib/TIFFRegisterCODEC.3t  lib/TIFFReverseBits.3t  lib/TIFFRGBAImageOK.3t
  lib/TIFFRGBAImageBegin.3t  lib/TIFFRGBAImageGet.3t  lib/TIFFRGBAImageEnd.3t  lib/TIFFSetErrorHandler.3t  lib/TIFFSetSubDirectory.3t 
 lib/TIFFSetWarningHandler.3t  lib/TIFFSwabArrayOfLong.3t  lib/TIFFSwabArrayOfShort.3t  lib/TIFFSwabLong.3t  lib/TIFFSwabShort.3t  lib
/TIFFScanlineSize.3t  lib/TIFFDefaultStripSize.3t  lib/TIFFVStripSize.3t  lib/TIFFStripSize.3t  lib/TIFFDefaultTileSize.3t  lib/TIFFVT
ileSize.3t  lib/TIFFTileSize.3t  lib/TIFFTileRowSize.3t  lib/TIFFUnRegisterCODEC.3t  lib/TIFFVGetField.3t  lib/TIFFVSetField.3t  lib/T
IFFReadBufferSetup.3t  lib/TIFFWriteBufferSetup.3t  
--- apps/Makefile ---
--- apps/tiffdither.1 ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/tiffdither.1 | nroff -man | compress > apps/tiffdither.1
--- apps/tiffdump.1 ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/tiffdump.1 | nroff -man | compress > apps/tiffdump.1
sh: nroff:  not found
--- apps/tiffdither.1 ---
sh: nroff:  not found
--- apps/tiffdump.1 ---
*** Error code 2
--- apps/tiffdither.1 ---
*** Error code 2
smake: Error: 2 errors
*** Error code 2
--- lib/Makefile ---
--- lib/TIFFPrintDirectory.3t ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/TIFFPrintDirectory.3t | nroff -man | compress > lib/TIFFPrintDirectory.3t
--- lib/TIFFOpen.3t ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/TIFFOpen.3t | nroff -man | compress > lib/TIFFOpen.3t
sh: nroff:  not found
--- lib/TIFFPrintDirectory.3t ---
sh: nroff:  not found
--- lib/TIFFReadDirectory.3t ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/TIFFReadDirectory.3t | nroff -man | compress > lib/TIFFReadDirectory.3t
sh: nroff:  not found
--- lib/TIFFReadEncodedStrip.3t ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/TIFFReadEncodedStrip.3t | nroff -man | compress > lib/TIFFReadEncodedStrip.3t
sh: nroff:  not found
--- lib/TIFFReadEncodedTile.3t ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/TIFFReadEncodedTile.3t | nroff -man | compress > lib/TIFFReadEncodedTile.3t
sh: nroff:  not found
--- lib/TIFFReadRGBAImage.3t ---
        sed -e 's;\${DIR_BIN};/usr/local/bin;g'  -e 's;\${DIR_LIB};/usr/local/lib;g'  -e 's;\${DIR_INC};/usr/local/include;g'   ../man
/TIFFReadRGBAImage.3t | nroff -man | compress > lib/TIFFReadRGBAImage.3t
sh: nroff:  not found
--- lib/TIFFReadEncodedTile.3t ---
*** Error code 2
smake: Error: 1 error
*** Error code 2
smake: Error: 2 errors
*** Error code 2
smake: Error: 1 error
Follow-Ups:
- Re: [ccp4bb]: Image production: in detail
  - From: Ravichandran Sankaranarayanan <sankaran@fas.harvard.edu>
- Re: [ccp4bb]: Image production: in detail
  - From: Ashley Buckle <ab@mrc-lmb.cam.ac.uk>
Prev by Date: [ccp4bb]: comparing shapes
Next by Date: [ccp4bb]: GIMP for image manipulation and a shameless plug for GNU in general ...
Prev by thread: [ccp4bb]: comparing shapes
Next by thread: Re: [ccp4bb]: Image production: in detail
Index(es):
- Date
- Thread