Hi Tom,
Just as Robert says, the quote should be dropped. Maybe you should've
had just one coffee more, but I should also have been more careful
typing. Apparently I usually automatically start of with typing
strings after .write( ;)
Sorry about that.
Tsjerk
On Fri, May 15, 2009 at 11:57 PM, Thomas Stout <tst...@exelixis.com> wrote:
>
>
> Hi Tsjerk --
>
> What version of PyMOL does this work with? I've been trying your commands
> with versions 1.1 and 1.2b and while PyMOL reports that the primitives have
> been processed, nothing is written to the file "protein.pov" other than the
> header info:
>
> camera {orthographic location <0.0 , 0.0 , 134.1048736572>
> look_at <0.0 , 0.0 , -1.0> right -74.9812240601*x up 59.9849815369*y}
> #default { finish{phong -1.000 ambient 0.500 diffuse 0.450
> phong_size 13
> .750000}}
> light_source{<4000.0001,4000.0001,9865.8951> rgb<1.0,1.0,1.0>}
> plane{z , -206.0869
> pigment{color rgb<1.0000,1.0000,1.0000>}
> finish{phong 0 specular 0 diffuse 0 ambient 1.0}}
> #include "povray.inc"
>
> and povray.inc contains:
> cmd.get_povray()[1]
>
> If I save a povray file with the GUI menu selection: File> Save Image As>
> POV-Ray
> then I get everything written to disk. This occurs on both linux and
> Windows.
>
> Am I missing something that would be more obvious if I had had more coffee
> today?
>
> Thanks!
> -Tom
>
> PS - There was a missing quotation mark:
> open("povray.inc","w").write("cmd.get_povray()[1]) -->
> open("povray.inc","w").write("cmd.get_povray()[1]")
>
>
>
> -----Original Message-----
> From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
> Sent: Thu 5/14/2009 1:47 PM
> To: Sean Law
> Cc: pymol-users
> Subject: Re: [PyMOL] POVRAY Usage
>
> Hi Sean,
>
> Unfortunately, getting a good image through POV-Ray requires editing
> the POV-Ray file. You can write the scene to disk with the following
> commands
>
> pov=open("protein.pov","w")
> pov.write(cmd.get_povray()[0])
> pov.write("#include \"povray.inc\"")
> pov.close()
>
> open("povray.inc","w").write("cmd.get_povray()[1])
>
> Then, take your favorite editor (under windows, you can use the
> POV-Ray editor) and make some changes:
>
> 1. There's a line starting with #defaults. Remove that and replace it with:
>
> #default {
> finish {
> ambient .15
> diffuse .5
> specular 1
> roughness .001
> reflection { .5 metallic } // Remove this line for less
> glossyness and faster tracing
> }
> }
>
> 2. There's a light statement, which says:
> light_source{<4000.0001,4000.0001,9960.0000> rgb<1.0,1.0,1.0>}.
> Replace it with:
>
> light_source
> {
> <20,10,0>
> rgb 2
> area_light <5,5,0>,5,5
> adaptive 1
> jitter
> }
>
> This usually works for me :)
>
> Note that the trace may now take some time. Remove the metallic
> reflection for faster tracing.
>
> I hope it helps. POV-Ray is cool, but rather complicated.
>
> Cheers,
>
> Tsjerk
>
> On Thu, May 14, 2009 at 10:21 PM, Sean Law <magic...@hotmail.com> wrote:
>>
>> Hi All,
>>
>> While ray tracing a scene with 10 x-large proteins in grid mode at 3600,
>> 3600 (width, height) I ran out of RAM (2 GB). I tried it again by writing
>> everything into a script and using pymol -qc which still ran out of memory.
>> I read somewhere that POVRAY is less of a memory hog so I installed the
>> latest version and simply modified my script to "ray 3600, 3600, renderer=1"
>> to use POVRAY. Everything went smoothly but I noticed that the image
>> generated from POVRAY looked different than the native ray traced structure
>> using PyMOL's ray tracer (simply invoking "ray" without dimensions in
>> PyMOL). Specifically, the light reflections appeared to be dulled in POVRAY
>> and spheres that were further away from the camera view are not
>> distinguishable. I've posted a comparison on the PyMOLWiki:
>>
>> http://www.pymolwiki.org/index.php/Povray_vs._pymol
>>
>> Firstly, I apologize as I am completely new to the world of POVRAY and I
>> just assumed that the image produced from either method would give
>> identical/close results but I much prefer the look of the PyMOL ray-tracer.
>> Is there an easy way to set everything up the same way as the PyMOL
>> ray-tracer but for POVRAY? Thank you for your time.
>>
>> Sean
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
> ------------------------------------------------------------------------------
> The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
> production scanning environment may not be a perfect world - but thanks to
> Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
> i700
> Series Scanner you'll get full speed at 300 dpi even with all image
> processing features enabled. http://p.sf.net/sfu/kodak-com
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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