Ah ha! Yes, of course.... Many thanks to you & Rob for catching that!
Note to self: *triple* shots of espresso next time.... :) -Tom -----Original Message----- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Saturday, May 16, 2009 1:30 AM To: Thomas Stout Cc: pymol-users Subject: Re: [PyMOL] POVRAY Usage 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 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. ------------------------------------------------------------------------------ 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
