> (gdb) r /usr/lib/python2.3/site-packages/pymol/__init__.py <your file>
>
>
> wait until the segfault, and call 'bt full' from gdb and send the
> output.
Here follows the gdb output.........
(gdb) r /usr/lib/python2.3/site-packages/pymol/__init__.py 3al1.pdb
Starting program: /usr/bin/python2.3 /usr/lib/python2.3/site-packages/pymol/__in
it__.py 3al1.pdb
(no debugging symbols found)
[Thread debugging using libthread_db enabled]
[New Thread 16384 (LWP 3688)]
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
PyMOL(TM) Molecular Graphics System, Version 0.97.
Copyright (C) 2004 by DeLano Scientific LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
Other Major Authors and Contributors:
Ralf W. Grosse-Kunstleve, Ph.D.
PyMOL is user-supported open-source software. Although most versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing campaign to create open and affordable software
for molecular research.
Updates and other information can be found at "http://www.pymol.org";.
Please cite PyMOL in publications and presentations:
Warren L. DeLano "The PyMOL Molecular Graphics System."
DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
(no debugging symbols found)
(no debugging symbols found)
OpenGL-based graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: Quadro4 750 XGL/AGP/SSE2
GL_VERSION: 1.5.3 NVIDIA 71.74
Hardware stereo capability detected.
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
[New Thread 32769 (LWP 3689)]
[New Thread 16386 (LWP 3690)]
[New Thread 32771 (LWP 3691)]
(no debugging symbols found)
(no debugging symbols found)
Adapting to Quadro hardware...
(no debugging symbols found)
(no debugging symbols found)
ObjectMolecule: read HELIX A 102 A 110
ObjectMolecule: read HELIX B 202 B 210
Crystal: Unit Cell 20.544 20.859 26.055
Crystal: Alpha Beta Gamma 101.160 97.030 118.060
Crystal: RealToFrac Matrix
Crystal: 0.0487 0.0259 0.0140
Crystal: 0.0000 0.0543 0.0163
Crystal: 0.0000 0.0000 0.0404
Crystal: FracToReal Matrix
Crystal: 20.5440 -9.8120 -3.1888
Crystal: 0.0000 18.4071 -7.4145
Crystal: 0.0000 0.0000 24.7734
Crystal: Unit Cell Volume 9368.
Symmetry: 1.00000 0.00000 0.00000 0.00000
Symmetry: 0.00000 1.00000 0.00000 0.00000
Symmetry: 0.00000 0.00000 1.00000 0.00000
Symmetry: 0.00000 0.00000 0.00000 1.00000
Symmetry: -1.00000 0.00000 0.00000 0.00000
Symmetry: 0.00000 -1.00000 0.00000 0.00000
Symmetry: 0.00000 0.00000 -1.00000 0.00000
Symmetry: 0.00000 0.00000 0.00000 1.00000
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 16384 (LWP 3688)]
0x4010d39b in mallopt () from /lib/libc.so.6
(gdb) bt full
#0 0x4010d39b in mallopt () from /lib/libc.so.6
No symbol table info available.
#1 0x4010c15f in free () from /lib/libc.so.6
No symbol table info available.
#2 0x404e910a in glXChannelRectSyncSGIX () from /usr/lib/libGL.so.1
No symbol table info available.
#3 0x08549108 in ?? ()
No symbol table info available.
#4 0x40af9e85 in _nv000845gl () from /usr/lib/libGLcore.so.1
No symbol table info available.
#5 0x08549108 in ?? ()
No symbol table info available.
#6 0x42faa040 in ?? ()
No symbol table info available.
#7 0x084fdd0c in ?? ()
No symbol table info available.
#8 0x0000034b in ?? ()
No symbol table info available.
#9 0xbffff088 in ?? ()
No symbol table info available.
#10 0x00000020 in ?? ()
No symbol table info available.
#11 0x42faa040 in ?? ()
No symbol table info available.
#12 0x085470b0 in ?? ()
No symbol table info available.
#13 0x0000034b in ?? ()
No symbol table info available.
#14 0xbffff088 in ?? ()
No symbol table info available.
#15 0x00000000 in ?? ()
No symbol table info available.
#16 0x00000000 in ?? ()
No symbol table info available.
#17 0x00000000 in ?? ()
No symbol table info available.
#18 0x00001ea8 in ?? ()
No symbol table info available.
#19 0x42ffd60c in ?? ()
No symbol table info available.
#20 0x42ffd654 in ?? ()
No symbol table info available.
#21 0x08299468 in ?? ()
No symbol table info available.
#22 0x00000000 in ?? ()
No symbol table info available.
#23 0x00000000 in ?? ()
No symbol table info available.
#24 0x00000000 in ?? ()
No symbol table info available.
#25 0x00000000 in ?? ()
No symbol table info available.
#26 0x00000004 in ?? ()
No symbol table info available.
#27 0x42ffb570 in ?? ()
No symbol table info available.
#28 0x42ffb570 in ?? ()
No symbol table info available.
#29 0x40afab0b in _nv000845gl () from /usr/lib/libGLcore.so.1
No symbol table info available.
#30 0x42faa040 in ?? ()
No symbol table info available.
#31 0x42faa040 in ?? ()
No symbol table info available.
#32 0x40af04ca in _nv000845gl () from /usr/lib/libGLcore.so.1
No symbol table info available.
#33 0x42faa040 in ?? ()
No symbol table info available.
#34 0x42faa040 in ?? ()
No symbol table info available.
#35 0x08548fd0 in ?? ()
No symbol table info available.
#36 0x08548fd0 in ?? ()
No symbol table info available.
#37 0x00000000 in ?? ()
No symbol table info available.
#38 0x084fb2a0 in ?? ()
No symbol table info available.
#39 0x42faa040 in ?? ()
No symbol table info available.
#40 0x40415438 in ?? () from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#41 0x084fdd0c in ?? ()
No symbol table info available.
#42 0x0000034b in ?? ()
No symbol table info available.
#43 0xbffff088 in ?? ()
No symbol table info available.
#44 0x404ae7db in ?? ()
No symbol table info available.
#45 0x403766a2 in RepWireBondRender ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#46 0x4031eee1 in CoordSetRender ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#47 0x40347bb1 in ObjectMoleculeRender ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#48 0x4030da44 in SceneScale ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#49 0x4030beea in SceneRender ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#50 0x402f0c19 in OrthoDoDraw ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#51 0x4038ca15 in ExecutiveDrawNow ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#52 0x403c46ed in was_main ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#53 0x403c4cd2 in was_main ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#54 0x405bace1 in fgJoystickPollWindow () from /usr/lib/libglut.so.3
No symbol table info available.
#55 0x405be43a in fgEnumWindows () from /usr/lib/libglut.so.3
No symbol table info available.
#56 0x405bad57 in fgJoystickPollWindow () from /usr/lib/libglut.so.3
No symbol table info available.
#57 0x405bbb6c in glutMainLoopEvent () from /usr/lib/libglut.so.3
No symbol table info available.
#58 0x405bbbf5 in glutMainLoop () from /usr/lib/libglut.so.3
No symbol table info available.
#59 0x403c3f3b in launch () from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#60 0x403c44ec in was_main ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#61 0x403b69ab in init_cmd ()
from /usr/lib/python2.3/site-packages/pymol/_cmd.so
No symbol table info available.
#62 0x080fde6a in PyCFunction_Call ()
No symbol table info available.
#63 0x080ab834 in PyEval_CallObjectWithKeywords ()
No symbol table info available.
#64 0x080a9bee in Py_MakePendingCalls ()
No symbol table info available.
#65 0x080ab96d in PyEval_CallObjectWithKeywords ()
No symbol table info available.
#66 0x080ab72c in PyEval_CallObjectWithKeywords ()
No symbol table info available.
#67 0x080a9bee in Py_MakePendingCalls ()
No symbol table info available.
#68 0x080aa77c in PyEval_EvalCodeEx ()
No symbol table info available.
#69 0x080acf79 in PyEval_EvalCode ()
No symbol table info available.
#70 0x080d90db in PyRun_FileExFlags ()
No symbol table info available.
#71 0x080d885f in PyRun_SimpleFileExFlags ()
No symbol table info available.
#72 0x08054e95 in Py_Main ()
No symbol table info available.
#73 0x080549eb in main ()
No symbol table info available.
(gdb) quit
The program is running. Exit anyway? (y or n) y
--
------------------------------------------------------------------------
Antoine M.M. Schreurs, BIJVOET Centre for Biomolecular Research
Laboratorium voor Kristal- en Structuurchemie, Universiteit Utrecht
Padualaan 8, 3584 CH Utrecht, the Netherlands
Telephone: +31-30-2533501 email: [EMAIL PROTECTED]
Fax: +31-30-2533940
------------------------------------------------------------------------
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