I'm not sure why this is causing problems with the extension menu, but it looks like your system configuration may be off for the "bad linux" system. So that might be a place to start. % glxinfo | grep vendor should give you some variant of NVIDIA. If not, check your Xorg.log (or xorg.conf).
Pete Martin Moche wrote: > 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]
