Hi Balaji,

In addition you can try the strategy I proposed earlier. Split your scene into separate objects and exdport them to povray one at a time (by turning all other objects off). In this way, you'll keep pymol from rendering the whole scene at once, which can lead to memory problems. Subsequently, you take one of the output .pov files and add an #include statement for each .inc file generated, thus combining them to a single povray scene. And then you pray that povray will be able to manage. With 1 or 2 Gb of ram and a good cpu you might get away with a large scene, though it may still take a while to render.

Tsjerk

On 1/25/06, Warren DeLano <warren@delsci.com> wrote:
Balaji,

One thing you might try is reducing "hash_max" to a smaller number -- 80
or even 50.  This will use less RAM but cause rendering to take much
much longer.

Cheers,
Warren

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Principal Scientist

. DeLano Scientific LLC
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> -----Original Message-----
> From: pymol-users-admin@lists.sourceforge.net
> [mailto:pymol-users-admin@lists.sourceforge.net] On Behalf Of
> Bhyravbhatla, Balaji
> Sent: Wednesday, January 25, 2006 9:50 AM
> To: Tsjerk Wassenaar
> Cc: pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] getting pov-ray temp files
>
> 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/pymol.com: 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?
>
>
>
> Thanks
>
>
>
> Balaji
>
>
>
> ________________________________
>
> From: Tsjerk Wassenaar [mailto: tsjerkw@gmail.com]
> Sent: Tuesday, January 24, 2006 3:41 PM
> To: Bhyravbhatla, Balaji
> Cc: pymol-users@lists.sourceforge.net
> 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 make_pov.py) 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!
>
> Tsjerk
>
> On 1/24/06, Bhyravbhatla, Balaji
> <Balaji.Bhyravbhatla@umassmed.edu > 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.
>
> Thanks
>
> Balaji
>
>
>
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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
>
>



--

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