----- Original Message ----- From: Scott Classen <[EMAIL PROTECTED]> Date: Friday, October 17, 2008 4:24 pm Subject: Fedora 8 binary core dumps - please help To: [email protected]
> Hi all I've attempting to install COOT 0.5 > I downloaded the stable tarball > > coot-0.5-binary-Linux-i386-fedora-8.tar.gz > > when I run the coot binary I get teh following error: > > COOT_PREFIX is /programs/coot-Linux-i386-fedora-8 > /programs/coot-Linux-i386-fedora-8/bin/coot-real > > 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 > /programs/coot-Linux-i386-fedora-8/share/coot/cootrc > /programs/coot-Linux-i386-fedora-8/share/coot/cootrc:31: error: > unexpectedidentifier `font_name', expected character `}' > INFO:: splash_screen_pixmap_dir > /programs/coot-Linux-i386-fedora-8/share/coot/pixmaps > INFO:: Colours file: > /programs/coot-Linux-i386-fedora-8/share/coot/colours.def loaded > There are 116 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/list/mon_lib_list.cifThere are 2 > data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/a/ALA.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/a/ASP.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/a/ASN.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/c/CYS.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/g/GLN.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/g/GLY.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/g/GLU.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/p/PHE.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/h/HIS.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/i/ILE.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/l/LYS.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/l/LEU.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/m/MET.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/m/MSE.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/p/PRO.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/a/ARG.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/s/SER.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/t/THR.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/v/VAL.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/t/TRP.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/t/TYR.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/p/PO4.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/s/SO4.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/g/GOL.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/e/ETH.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/c/CIT.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/a/AR.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/a/AD.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/c/CR.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/c/CD.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/g/GR.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/g/GD.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/t/TD.cifThere are 2 data in > /programs/coot-Linux-i386-fedora- > 8/share/coot/lib/data/monomers/u/UR.cifReading coordinate file: > /programs/coot-Linux-i386-fedora-8/share/coot/standard-residues.pdb > PDB file > /programs/coot-Linux-i386-fedora-8/share/coot/standard-residues.pdb > has been > read. > Spacegroup: P 1 > Cell: 40.631 109.18 93.243 90 90 90 > CATASTROPHIC ERROR:: in gl_extras no GtkGL widget! > CATASTROPHIC ERROR:: failed to create Gtk GL widget (Check that > your X11 > server is working and has (at least) "Thousands of Colors" and > supports GLX.) > initalize graphics molecules...done. > (filter-fileselection-filenames-state) > (get-active-map-drag-flag) > (use-graphics-interface-state) > Loading scheme files from /programs/coot-Linux-i386-fedora- > 8/share/coot/schemeload "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 root. Welcome to Coot. > (set-display-intro-string "Good afternoon root. 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" > /programs/coot-Linux-i386-fedora-8/bin/coot: line 124: 30192 > Segmentationfault $coot_real $* > coot-exe: "/programs/coot-Linux-i386-fedora-8/bin/coot-real" > coot-version: > /programs/coot-Linux-i386-fedora-8/bin/coot-real > core: #f > No core file found. No debugging > > > > any suggestions? Am I missing some dependencies? > OK I also tried installing the gtk2 python version. coot-0.5-binary-Linux-i386-fedora-8-python-gtk2.tar.gz This time it sorta launches, but nothing displays and I ge the following errors: (coot-real:30973): GtkGLExt-WARNING **: cannot create GdkGLContext (coot-real:30973): GdkGLExt-CRITICAL **: gdk_gl_window_impl_x11_make_context_current: assertion `GDK_IS_GL_CONTEXT_IMPL_X11 (glcontext)' failed Ack!!
