Re: [PyMOL] pymol raytracing crash

[Thomas Siegmund]

Dear Warren,

I installed it with python distutils from source. See the bug report I filed 
in the meantime for details. It turned out to be a problem with some versions 
of gcc - crash when raytracing lines, sticks or meshes with gcc (GCC) 3.3 
20030226 (prerelease) (SuSE Linux) and with gcc 3.3.1, but a perfectly 
stable PyMOL with good old gcc 2.95.3.

Best regards

Thomas

Am Dienstag, 16. September 2003 00:37 schrieb Warren L. DeLano:
 Thomas,

   I tried running your script on the current development version
 and on a version 0.90 binary, and wasn't able to get PyMOL to crash.

   How is PyMOL installed on your system?

 Cheers,
 Warren

 --
 mailto:war...@delanoscientific.com
 Warren L. DeLano, Ph.D.
 Principal Scientist
 DeLano Scientific LLC
 Voice (650)-346-1154
 Fax   (650)-593-4020

  -Original Message-
  From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
  ad...@lists.sourceforge.net] On Behalf Of Thomas Siegmund
  Sent: Wednesday, September 10, 2003 6:16 AM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] pymol raytracing crash
 
 
 
  Hi everybody,
 
  I am new to pymol. So maybe I'm doing something wrong, but pymol

 almost

  everytime crashes when I try to raytrace a picture. I had some success
  with
  small protein structures in cartoon representation. The same molecule

 in


-- 
Thomas Siegmund, Ph.D.
DeveloGen AG
Bioinformatics and Data Management
Phone: +49(551) 505 58 651

E-Mails können unvollst

RE: [PyMOL] pymol raytracing crash

[Warren L. DeLano]

Thomas,

I tried running your script on the current development version
and on a version 0.90 binary, and wasn't able to get PyMOL to crash.

How is PyMOL installed on your system?

Cheers,
Warren

--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Thomas Siegmund
 Sent: Wednesday, September 10, 2003 6:16 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] pymol raytracing crash
 


 Hi everybody,
 
 I am new to pymol. So maybe I'm doing something wrong, but pymol
almost
 everytime crashes when I try to raytrace a picture. I had some success
 with
 small protein structures in cartoon representation. The same molecule
in
 lines or sticks representation crashes the pymol raytracer.
 
 Here some console output:
 
 siegm...@siegmund:~ /usr/local/bin/python
 /usr/local/lib/python2.3/site-packages/pymol/__init__.py -x
 /tmp/pymol/7LYZ.pdb
 
  PyMOL(TM) Molecular Graphics System, Version 0.90.
  Copyright (C) 1998-2003 by DeLano Scientific LLC.
 // I cut some lines here
  OpenGL based graphics front end:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: RIVA TNT2/AGP/SSE2
   GL_VERSION: 1.4.0 NVIDIA 44.96
  PDBStrToCoordSet: Attempting to read symmetry information
  Crystal: Unit Cell   27.400   31.900   34.400
  Crystal: Alpha Beta Gamma88.000  108.000  112.000
  Crystal: RealToFrac Matrix
  Crystal:0.03650.01470.0133
  Crystal:0.0.03380.0031
  Crystal:0.0.0.0307
  Crystal: FracToReal Matrix
  Crystal:   27.4000  -11.9500  -10.6302
  Crystal:0.   29.5772   -3.
  Crystal:0.0.   32.5785
  Crystal: Unit Cell Volume26402.
  Symmetry:  1.0  0.0  0.0  0.0
  Symmetry:  0.0  1.0  0.0  0.0
  Symmetry:  0.0  0.0  1.0  0.0
  Symmetry:  0.0  0.0  0.0  1.0
  Executive: object 7LYZ created.
 PyMOLutil.ss
  util.ss: WARNING: This is not a correct secondary structure
 // I cut some lines here
  util.ss: assignment complete.
 PyMOLhide lines
 PyMOLshow cartoon
 PyMOLray
  Ray: total time: 1.14 sec. = 3145.7 frames/hour. (1.15 sec. accum.)
 PyMOLhide cartoon
 PyMOLshow sticks
 PyMOLray
 Speicherzugriffsfehler (segmentation fault)
 
 Pymol is version 0.9, installed from source package on SuSE linux 8.2.
To
 make
 sure that it is not a problem of the python installation (standard
SuSE
 8.2
 rpm, python-2.2.2) I installed python 2.3 from source. Same result. In
the
 mailing list archive I found comments about memory usage for
raytracing.
 This
 machine has 500 MB RAM. Top shows about 150-200 MB free RAM and 1GB
 untouched
 swap just before the raytracing. I tried the command set hash_max,
60 as
 recommended, but this also did not help.
 
 Any hints?
 
 Tanks for your help
 
 Thomas
 
 --
 Thomas Siegmund, Ph.D.
 DeveloGen AG
 Bioinformatics and Data Management
 Phone: +49(551) 505 58 651
 
 
 
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