Thanks Tsjerk,

I still have the same issue of PyMOL aborting on me:


RayRenderPovRay: processed 2956434 graphics primitives.

VLAExpand-ERR: realloc failed.

****EEK! PyMOL just ran out of memory and crashed


/usr/local/pymol/ line 14: 3812 Aborted



So I guess I really need to look for larger resources (hardware) meanwhile is it possible to use PyMOL on a command line and have it write out the output files? What I had in mind was to install PyMOL on our cluster (Opteron based) that has 8GB RAM on the node and submit it without the invocation of the GUI? The cluster does only computations and no graphics as most clusters are. Will it work?






From: Tsjerk Wassenaar []
Sent: Tuesday, January 24, 2006 3:41 PM
To: Bhyravbhatla, Balaji
Subject: Re: [PyMOL] getting pov-ray temp files


Hi Balaji,

The temporary povray file is written to the working directory. However, you may want to use the attached script instead. This will write your scene in two parts, a .pov file containing all meta data, such as the lights, camera and #defaults, and an include file (.inc) which contains the structure. In this way you have maximum control over your scene without having to edit a huge povray file. You may even want to consider splitting your scene up in separate parts (taken from the same perspective), which you combine in a global .pov file using #include statements. This will give even more control with regards to modifications to the scene.

The magic word in pymol (after run is make_pov

NB. the .pov file contains a commented statement with regards to a povray script, which allows transforming scenes and objects from model space to camera space and vice versa. If you want, you can get a copy of that script.

Good luck!


On 1/24/06, Bhyravbhatla, Balaji < > wrote:

Hello All,
I am trying to render a large mega Dalton complex and can get it up on
the screen but rendering it causes a crash because of memory issues (I
have 1Gb on the system and tried on a 2Gb system also). So what I would
like is to get the temp pov ray files that Pymol is writing out and use
those with PoVRAY.
I am unable to find the location of those files. Can you please point me
to where they are written?

If anyone also has ideas on how to get a decent publication quality
output for a complex (think in terms of viruses) that would be helpful.
I do have a session file saved with my views.



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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336