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 >> >> ________________________________ >> Help keep personal info safe. Get Internet Explorer 8 today! >> >> ------------------------------------------------------------------------------ >> 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 >> _______________________________________________ >> PyMOL-users mailing list >> PyMOL-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > > > -- > 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 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > This email (including any attachments) may contain material > that is confidential and privileged and is for the sole use of > the intended recipient. Any review, reliance or distribution by > others or forwarding without express permission is strictly > prohibited. If you are not the intended recipient, please > contact the sender and delete all copies. > Exelixis, Inc. reserves the right, to the extent and under > circumstances permitted by applicable law, to retain, monitor > and intercept e-mail messages to and from its systems. > > -- 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 ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users