Hello, Desktop effects are NOT turned on. ccp4i 6.0.2 works fine.
I just tried the latest nightly and that didn't work either coot-0.5.1-pre-1-revision-1502-binary-Linux-i386-fedora-8-python-gtk2.tar.gz I have a hunch this has something to do with my graphics card. I have an NVIDIA card (GeForce FX 5200) I've installed the nvidia linux drivers NVIDIA Driver Version 169.12 Scott ----- Original Message ----- From: Iain Kerr <[EMAIL PROTECTED]> Date: Friday, October 17, 2008 4:47 pm Subject: Re: Fedora 8 binary core dumps - please help To: COOT@JISCMAIL.AC.UK > Hi Scott, > > Is X11 running correctly ? (check if CCP4i launches)..it should > work out > the box in F8. > > Do you have the desktop effects switched on (wobbly windows etc.) ? > At > least earlier versions of Coot wouldn't launch properly under > Fedora > while desktop effects/Compiz/Beryl etc. were running.. > > HTH, > Iain > > Scott Classen wrote: > > ----- Original Message ----- > > From: Scott Classen <[EMAIL PROTECTED]> > > Date: Friday, October 17, 2008 4:24 pm > > Subject: Fedora 8 binary core dumps - please help > > To: COOT@JISCMAIL.AC.UK > > > > > >> 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!! > > > > >
