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
