Re: [PyMOL] pymol raytracing crash
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
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. > 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 > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Transparent cartoons?
Christian, Transparent cartoons have been implemented, but not yet released excepted in the latest G4/G5 Mac demo version. If you have a Mac, you can set cartoon_transparency, 0.5 using that version. Note that cartoon transparency is really only useful when ray-tracing, because visual artifacts will occur with standard OpenGL rendering. If you're on a PC, then you'll need to wait for the next big release, which will probably happen next week. 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 Christian Siebold > Sent: Monday, September 15, 2003 10:11 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Transparent cartoons? > > Dear Pymol users > > How can I create transparent cartoon? > I tried to use the transparency option from the "setting" panel, but > this only worked for surfaces and not for cartoons. > > Thanks a lot, > Christian > > > -- > Dr. Christian Siebold > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > University of Oxford > Roosevelt Drive, Oxford OX3 7BN, UK > > Tel: (+44)-1865-287550 > Fax: (+44)-1865-287547 > Email: christ...@strubi.ox.ac.uk > Website: http://www.strubi.ox.ac.uk > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Transparent cartoons?
Dear Pymol users How can I create transparent cartoon? I tried to use the transparency option from the "setting" panel, but this only worked for surfaces and not for cartoons. Thanks a lot, Christian -- Dr. Christian Siebold Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Tel: (+44)-1865-287550 Fax: (+44)-1865-287547 Email: christ...@strubi.ox.ac.uk Website: http://www.strubi.ox.ac.uk
