Anton, Thanks for sending the data along -- it turns out that there's a practical limit to how complex an image you can generate in PyMOL and then send via Python. You're simply running out of RAM!
As shown in your output, a 70S ribosome with default PyMOL settings involves over 1 million graphics primitives. PyMOL itself needs about 500 MB for the graphics information, and the POVray input file requires hundreds of bytes per primitive. It's quite easy to exceed 1 GB of RAM usage in such situations. But if you set cartoon_sampling, 3 set cartoon_loop_quality, 5 set cartoon_tube_quality, 5 You'll get that number down to a more manageable 330,000 primitives. The POVray input file will only be about 181 MB then, and it should be possible to passage this through Python as a string without blowing out your RAM. PovRay itself can just barely handle such a large input file -- it'll need about 750 MB for rendering. Oh -- I forget to mention that PyMOL 0.98beta05 requires PovRay 3.5 or better. "ray renderer=2" will render using PovRay automatically if "povray" is in the path. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: av...@lbl.gov [mailto:av...@lbl.gov] > Sent: Thursday, September 09, 2004 12:59 PM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: light source inside a molecule?? > > I'm trying to render a 70S ribosome molecule (about 140,000 > atoms) with povray by using a "make_pov.py" > script as the one described by Scott Classen earlier on in > this thread. I got the whole process to work with a line > model of the 70S but when I create a cartoon model of the > ribosome pymol crashes at the make_pov('povray.inp') stage. > Here is the output of a run with the new beta version > > %%%%% > > pymol-0_98beta05/pymol/pymol.com -c log-pvr > ay-test.pml > > PyMOL(TM) Molecular Graphics System, Version 0.98beta05. > Copyright (C) 2004 by DeLano Scientific LLC. > All Rights Reserved. > > Created by Warren L. DeLano, Ph.D. > > Other Major Authors and Contributors: > > Ralf W. Grosse-Kunstleve, Ph.D. > > PyMOL is user-supported open-source software. > Although most versions > are freely available, PyMOL is not in the public domain. > > If PyMOL is helpful in your work or study, then please volunteer > support for our ongoing campaign to create open and > affordable software > for molecular research. > > Updates and other information can be found at > "http://www.pymol.org";. > > Please cite PyMOL in publications and presentations: > > Warren L. DeLano "The PyMOL Molecular Graphics System." > DeLano Scientific LLC, San Carlos, CA, USA. > http://www.pymol.org > > Enter "help" for a list of commands. > Enter "help <command-name>" for information on a specific command. > > Hit ESC anytime to toggle between text and graphics. > > Command mode. No graphics front end. > PyMOL>load log-test-povray.pse > Executive: Loading version 0.95 session... > PyMOL>run make_pov.py > PyMOL>make_pov('test_molecule.pov') > RepSurface: 8875 surface points. > RepSurface: 14190 triangles. > RepSurface: 8875 surface points. > RepSurface: 14190 triangles. > RayRenderPOV: w 640 h 480 f 760.232 b 1001.270 > RayRenderPOV: vol -383.479 383.479 -287.610 > RayRenderPOV: vol 287.610 760.232 1001.270 > RayRenderPovRay: processed 1115684 graphics primitives. > pymol-0_98beta05/pymol/pymol.com: line 14: 8439 > Segmentation fault (core dumped) > $PYMOL_PATH/pymol.exe $* > %%%%% > > and here is the same output with version 0.95 > > %%%%% > > pymol -c log-pvray-test.pml > > > PyMOL(TM) Molecular Graphics System, Version 0.95. > Copyright (C) 2004 by DeLano Scientific LLC. > All Rights Reserved. > > Created by Warren L. DeLano, Ph.D. > > Other Major Authors and Contributors: > > Ralf W. Grosse-Kunstleve, Ph.D. > > PyMOL is user-supported open-source software. > Although most versions > are freely available, PyMOL is not in the public domain. > > If PyMOL is helpful in your work or study, then please volunteer > support for our ongoing campaign to create open and > affordable software > for molecular research. > > Updates and other information can be found at > "http://www.pymol.org";. > > Please cite PyMOL in publications and presentations: > > Warren L. DeLano "The PyMOL Molecular Graphics System." > DeLano Scientific LLC, San Carlos, CA, USA. > http://www.pymol.org > > Enter "help" for a list of commands. > Enter "help <command-name>" for information on a specific command. > > Hit ESC anytime to toggle between text and graphics. > > Command mode. No graphics front end. > PyMOL>load log-test-povray.pse > Executive: Loading version 0.95 session... > PyMOL>run make_pov.py > PyMOL>make_pov('test_molecule.pov') > RepSurface: 8874 surface points. > RepSurface: 14194 triangles. > RepSurface: 8874 surface points. > RepSurface: 14194 triangles. > RayRenderPOV: w 640 h 480 f 760.232 b 1001.270 > RayRenderPOV: vol -383.479 383.479 -287.610 > RayRenderPOV: vol 287.610 760.232 1001.270 > RayRenderPovRay: processed 1115688 graphics primitives. > Segmentation fault (core dumped) > %%%%% > > Any suggestions? > > Anton > > > >
