Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

[Christian S. <cse...@bp...>]

$PYTHONPATH is not set on my machine.



You wrote:

      Re: segmentation fault after switching mainwindow between visualisation 
and commandline
      From: Martin <martin.hoefling@gm...> - 2006-11-13 05:15

       ... i had a similar Problem this morning. What is your PYTHONPATH? For 
me, 
       unsetting it solved the problems.
       
       Cheers	
       	Martin
       


segmentation fault after switching mainwindow between visualisation and 
commandline
From: Christian Seifert <cseifert@bp...> - 2006-11-13 02:07

 Hi,
 
 I found a critical and reproducible bug using the 0.99rc6-binarys on my
 machine.
 
 Stepps:
 - starting pymol from a kde terminal with user-rights
 - loading a pdb-file (e.g. 1K5D from pdb-database)
 - rotate the molecule with the mouse in any direction
 - hitting "Esc" to get to the commandline-mode
 - hitting "Esc" again to get back to the visualisation-mode
 - trying to rotate the molecule again with the mouse
 
 The programm crashes, the two windows of pymol disappear and my
 terminal-window show the following error:
 
 >./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe "$@"
 
 "Speicherzugriffsfehler" is the german word for segmentation fault.
 
 There is nothing in dmseg.
 
 The full output:
 >cseifert@lexx ~/pymol $ ./pymol
 >
 > PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
 >
 > A current PyMOL Maintenance and/or Support Subscription may be required
 > for legal use of this Build beyond a finite honor-system evaluation period.
 > Please visit http://www.pymol.org/funding.html for more information.
 >
 > This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
 > OpenGL graphics engine:
 >  GL_VENDOR: ATI Technologies Inc.
 >  GL_RENDERER: ATI MOBILITY FireGL V5200 Pentium 4 (SSE2) (FireGL) (GNU_ICD)
 >  GL_VERSION: 2.0.5946 (8.27.10)
 > Detected 2 CPUs.  Enabled multithreaded rendering.
 >HEADER    SIGNALING PROTEIN/SIGNALING ACTIVATOR   10-OCT-01   1K5D
 >TITLE     CRYSTAL STRUCTURE OF RAN-GPPNHP-RANBP1-RANGAP COMPLEX
 >COMPND    MOL_ID: 1;
 >COMPND   2 MOLECULE: GTP-BINDING NUCLEAR PROTEIN RAN;
 >COMPND   3 CHAIN: A, D, G, J;
 >COMPND   4 SYNONYM: RAN, TC4, RAN GTPASE, ANDROGEN RECEPTOR-
 >COMPND   5 ASSOCIATED PROTEIN 24;
 >COMPND   6 ENGINEERED: YES;
 >COMPND   7 MOL_ID: 2;
 >COMPND   8 MOLECULE: RAN-SPECIFIC GTPASE-ACTIVATING PROTEIN;
 >COMPND   9 CHAIN: B, E, H, K;
 >COMPND  10 SYNONYM: RANBP1, RAN BINDING PROTEIN 1;
 >COMPND  11 ENGINEERED: YES;
 >COMPND  12 MUTATION: YES;
 >COMPND  13 MOL_ID: 3;
 >COMPND  14 MOLECULE: RAN GTPASE ACTIVATING PROTEIN 1;
 >COMPND  15 CHAIN: C, F, I, L;
 >COMPND  16 SYNONYM: RANGAP, PROTEIN RNA1;
 >COMPND  17 ENGINEERED: YES
 > ObjectMolecule: Read secondary structure assignments.
 > ObjectMolecule: Read crystal symmetry information.
 > Symmetry: Found 1 symmetry operators.
 > CmdLoad: "/home/cseifert/Desktop/1K5D.pdb" loaded as "1K5D".
 >./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe "$@"
 
 Thanks,
 
 Christian Seifert.