Dear Coot Users, When running coot from a Linux server the startup looks different between two Linux clients. At one client I got the extensions menu but not on the other, so I suppose the difference is due to local settings varying between the two clients. By comparing the two coot startup files I hope somebody can explain what the problem is.
Please note below that the BAD Linux do not recognise my graphics NVIDIA card? VENDOR : SGI VERSION : 1.4 % lspci | grep VGA 05:00.0 VGA compatible controller: nVidia Corporation NV41GL (rev a2) however at the Good Linux VENDOR : NVIDIA Corporation VERSION : 1.3 % lspci | grep VGA 05:00.0 VGA compatible controller: nVidia Corporation: Unknown device 00ce (rev a2) At the BAD linux I got the following "extra" error messages: Gtk-WARNING **: Unable to locate loadable module in module_path: "libgalaxy.so", load "extensions.scm" (Error in proc: unbound-variable args: (#f Unbound variable: ~S (gtk-menu-item-submenu) #f)) Thanks for you assistance, Martin ################ BAD Linux Startup ####################### daffy-mochma 23% coot COOT_PREFIX is /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0 /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real: /usr/X11R6/lib/libGL.so.1: no version information available (required by /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real) /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real: /usr/X11R6/lib/libGL.so.1: no version information available (required by /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/lib/libgtkgl.so.5) /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real: /usr/X11R6/lib/libGL.so.1: no version information available (required by /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/lib/libglut.so.3) If have found this software to be useful, you are requested to cite: Coot: model-building tools for molecular graphics Emsley P, Cowtan K ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2126-2132 Part 12 Sp. Iss. 1 DEC 2004 The reference for the REFMAC5 Dictionary is: REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S, Long F, Murshudov GN ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2184-2195 Part 12 Sp. Iss. 1 DEC 2004 If using "SSM Superposition", please cite: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Krissinel E, Henrick K ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2256-2268 Part 12 Sp. Iss. 1 DEC 2004 Acquiring application resources from /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/cootrc Gtk-WARNING **: Unable to locate loadable module in module_path: "libgalaxy.so", Gtk-WARNING **: Unable to locate loadable module in module_path: "libgalaxy.so", Gtk-WARNING **: Unable to locate loadable module in module_path: "libgalaxy.so", Gtk-WARNING **: Unable to locate loadable module in module_path: "libgalaxy.so", /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/cootrc:31: error: unexpected identifier `font_name', expected character `}' INFO:: splash_screen_pixmap_dir /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/pixmaps INFO:: Colours file: /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/colours.def loaded INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers/ There are 117 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//list/mon_lib_list.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ALA.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ASP.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ASN.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CYS.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GLN.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GLY.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GLU.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//p/PHE.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//h/HIS.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//i/ILE.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//l/LYS.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//l/LEU.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//m/MET.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//m/MSE.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//p/PRO.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ARG.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//s/SER.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/THR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//v/VAL.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/TRP.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/TYR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//p/PO4.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//s/SO4.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GOL.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//e/ETH.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CIT.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/AR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/AD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/TD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//u/UR.cif Reading coordinate file: /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/standard-residues.pdb PDB file /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 VENDOR : SGI VERSION : 1.4 EXTENSIONS : GLX_ARB_get_proc_address GLX_ARB_multisample GLX_EXT_import_context GLX_EXT_visual_info GLX_EXT_visual_rating GLX_MESA_allocate_memory GLX_MESA_swap_control GLX_MESA_swap_frame_usage GLX_OML_swap_method GLX_OML_sync_control GLX_SGI_make_current_read GLX_SGI_swap_control GLX_SGI_video_sync GLX_SGIS_multisample GLX_SGIX_fbconfig GLX_SGIX_pbuffer GLX_SGIX_visual_select_group initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/scheme load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "coot-gui.scm" Coot Scheme Scripting GUI code found and loaded. load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" load "local-code.scm" load "hello.scm" Good afternoon Martin Moche. Welcome to Coot. (set-display-intro-string "Good afternoon Martin. Welcome to Coot") load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "americanisms.scm" load "group-settings.scm" (set-display-lists-for-maps 0) load "tips-gui.scm" load "extensions.scm" (Error in proc: unbound-variable args: (#f Unbound variable: ~S (gtk-menu-item-submenu) #f)) (use-graphics-interface-state) (coot-checked-exit 0) (clear-backups-maybe) There are 0 old files (0 bytes) (0.0Mb) in "coot-backup" (stereo-mode-state) State file 0-coot.state.scm written. (save-state) State file 0-coot-history.py written. State file 0-coot-history.scm written. ############################ Good Linux startup ######################## bruce-mochma 19% coot COOT_PREFIX is /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0 /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real: /usr/X11R6/lib/libGL.so.1: no version information available (required by /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real) /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real: /usr/X11R6/lib/libGL.so.1: no version information available (required by /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/lib/libgtkgl.so.5) /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/bin/coot-real: /usr/X11R6/lib/libGL.so.1: no version information available (required by /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/lib/libglut.so.3) If have found this software to be useful, you are requested to cite: Coot: model-building tools for molecular graphics Emsley P, Cowtan K ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2126-2132 Part 12 Sp. Iss. 1 DEC 2004 The reference for the REFMAC5 Dictionary is: REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S, Long F, Murshudov GN ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2184-2195 Part 12 Sp. Iss. 1 DEC 2004 If using "SSM Superposition", please cite: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Krissinel E, Henrick K ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2256-2268 Part 12 Sp. Iss. 1 DEC 2004 Acquiring application resources from /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/cootrc /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/cootrc:31: error: unexpected identifier `font_name', expected character `}' Loading required GL library /usr/lib/libGL.so.1 INFO:: splash_screen_pixmap_dir /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/pixmaps INFO:: Colours file: /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/colours.def loaded INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers/ There are 117 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//list/mon_lib_list.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ALA.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ASP.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ASN.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CYS.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GLN.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GLY.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GLU.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//p/PHE.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//h/HIS.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//i/ILE.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//l/LYS.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//l/LEU.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//m/MET.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//m/MSE.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//p/PRO.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/ARG.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//s/SER.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/THR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//v/VAL.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/TRP.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/TYR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//p/PO4.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//s/SO4.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GOL.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//e/ETH.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CIT.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/AR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//a/AD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//c/CD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GR.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//g/GD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//t/TD.cif There are 2 data in /net/fileserver/xtal/ccp4-6.0.2/lib/data/monomers//u/UR.cif Reading coordinate file: /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/standard-residues.pdb PDB file /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 Loading required GL library /usr/lib/libGL.so.1 VENDOR : NVIDIA Corporation VERSION : 1.3 EXTENSIONS : GLX_ARB_get_proc_address GLX_ARB_multisample GLX_EXT_visual_info GLX_EXT_visual_rating GLX_EXT_import_context GLX_SGI_video_sync GLX_NV_swap_group GLX_NV_video_out GLX_SGIX_fbconfig GLX_SGIX_pbuffer GLX_SGI_swap_control GLX_NV_float_buffer initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /net/fileserver/xtal/graphics/coot-Linux-i386-redhat-8.0/share/coot/scheme load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "coot-gui.scm" Coot Scheme Scripting GUI code found and loaded. load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" load "local-code.scm" load "hello.scm" Good afternoon Martin Moche. Welcome to Coot. (set-display-intro-string "Good afternoon Martin. Welcome to Coot") load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "americanisms.scm" load "group-settings.scm" (set-display-lists-for-maps 0) load "tips-gui.scm" load "extensions.scm" (use-graphics-interface-state) (coot-checked-exit 0) (clear-backups-maybe) There are 0 old files (0 bytes) (0.0Mb) in "coot-backup" (stereo-mode-state) State file 0-coot.state.scm written. (save-state) State file 0-coot-history.py written. State file 0-coot-history.scm written. ################### Good Linux startup END ########################### __________________________________________________ Martin Moche, Ph.D., M.Sc. Senior scientist Karolinska Institutet MBB/SGC Scheeles väg 2 171 77 Stockholm Sweden Phone: +46-8-524 868 43 Mob: +46-733-229327 Fax: +46-8-524 868 68 [EMAIL PROTECTED]
