Re: [COOT] Fedora 8 binary core dumps - please help

Fri, 17 Oct 2008 16:47:28 -0700 

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: [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!!


  






















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