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 Gamma 88.000 108.000 112.000
> Crystal: RealToFrac Matrix
> Crystal: 0.0365 0.0147 0.0133
> Crystal: 0.0000 0.0338 0.0031
> Crystal: 0.0000 0.0000 0.0307
> Crystal: FracToReal Matrix
> Crystal: 27.4000 -11.9500 -10.6302
> Crystal: 0.0000 29.5772 -3.0000
> Crystal: 0.0000 0.0000 32.5785
> Crystal: Unit Cell Volume 26402.
> 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
> Executive: object "7LYZ" created.
> PyMOL>util.ss
> util.ss: WARNING: This is not a "correct" secondary structure
> // I cut some lines here
> util.ss: assignment complete.
> PyMOL>hide lines
> PyMOL>show cartoon
> PyMOL>ray
> Ray: total time: 1.14 sec. = 3145.7 frames/hour. (1.15 sec. accum.)
> PyMOL>hide cartoon
> PyMOL>show sticks
> PyMOL>ray
> 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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