Did you try using POV-Ray with PyMOL to do the ray tracing?
renderer = 1 uses PovRay's renderer. This is Unix-only and you must have
"povray" in your path. It utilizes two temporary files: "tmp_pymol.pov" and
"tmp_pymol.png". Also works on Mac via Povray37UnofficialMacCmd but it needs
to be in your path as "povray".
Jim
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From: Stephen Kerry [mailto:stephen.kerr...@outlook.com]
Sent: Monday, May 09, 2016 8:35 PM
To: David Hall <li...@cowsandmilk.net>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing
Thank you for trying this out on a workstation with 128 GB and then 256 GB
of RAM. It is much appreciated as I do not have easy access to that kind of
computational power. The fact that you also get these segfaults with all of
your RAM, suggests that this might be a PyMOL limitation, rather than a
hardware issue.
I have come to the conclusion that it is impossible to ray trace an image
with an output resolution greater than 45 megapixels (7500 x 6000). Halving
the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution.
I was wondering if the developers have come across this upper limit too? I
have a 2400 dpi printer, so I want to go with the highest dpi possible for
the best quality.
_____
From: David Hall <li...@cowsandmilk.net <mailto:li...@cowsandmilk.net> >
Sent: 06 May 2016 19:17:38
To: Stephen Kerry
Cc: pymol-users@lists.sourceforge.net
<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] High Resolution Ray Tracing
Feel free to send me the files off list.
-David Hall
On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com
<mailto:stephen.kerr...@outlook.com> > wrote:
Dear All,
I have a protein complex scene that I need to create a large, high
resolution (1200 dpi) ray traced image of, but am unable to do so as I
always run out of memory at the end of the ray tracing process, with the
following error:
python2.7(972,0x7fff7397f300) malloc: ***
mach_vm_map(size=18446744068907188224) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor
and 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than
twice this reserved for virtual memory, but no swap is actually used.
Decreasing hash_max just increases the ray tracing time until the error at
the end. Sometimes PyMOL will be terminated with this error, whilst at other
times a transparent PNG is all that is produced.
Is there a way to force PyMOL to use virtual memory to avoid these
errors/crashes at the expense of processing time?
If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB
or more RAM, who would be able to render this ray traced image if I send
the, the .pse file and .pml script off list? Takes about 10 mins to process.
Cheers,
Stephen
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