[PyMOL] Color coded script

2016-05-09 Thread mark . zierden
Hi, In the PyMolWiki under simple scripting parts of the command lines are color coded(red, blue and green). What does that mean? cmd.extend(“doSimpleThing”,doSimpleThing)-- Find and fix application performance issues fa

Re: [PyMOL] Color coded script

2016-05-09 Thread Julian Heinrich
Hi, are you referring to the code examples? I think the coloring scheme is just a source code syntax highlighting, where all strings for example are in red, comments are in green, and functions are blue. Cheers, Julian On Tue, Nov 10, 2015 at 3:15 PM, wrote: > Hi, > > In the PyMolWiki under si

[PyMOL] Iterate scenes smoothly

2016-05-09 Thread Leandro Bortot
Dear users, I'm trying to make a movie during which a surface changes its color. I followed the tutorials from the wiki and successfully created two scenes with the desired colors. However, I can't make them iterate smoothly. Instead, The first half of the frames display the first scene

Re: [PyMOL] Iterate scenes smoothly

2016-05-09 Thread harold steinberg
that’s the same result I always get… > On May 9, 2016, at 12:23 PM, Leandro Bortot wrote: > > Dear users, > > I'm trying to make a movie during which a surface changes its color. I > followed the tutorials from the wiki and successfully created two scenes with > the desired colors. >

Re: [PyMOL] Iterate scenes smoothly

2016-05-09 Thread João M . Damas
Not sure it works, but if the colors are related to some parameter, try this: http://www.pymolwiki.org/index.php/Morph On Mon, May 9, 2016 at 7:26 PM, harold steinberg wrote: > that’s the same result I always get… > > On May 9, 2016, at 12:23 PM, Leandro Bortot wrote: > > Dear users, > >

Re: [PyMOL] High Resolution Ray Tracing

2016-05-09 Thread Stephen Kerry
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

Re: [PyMOL] High Resolution Ray Tracing

2016-05-09 Thread Takanori Nakane
Hi, By tweaking the projection matrix, we can divide a big scene into several sub-images and render them separately. Thus, we can reduce the memory consumption. I think this is scriptable, although I don't have time to implement myself. > I was wondering if the developers have come across this u

Re: [PyMOL] High Resolution Ray Tracing

2016-05-09 Thread harold steinberg
I can try to address the 2400 dpi printer resolution. Printer manufactures specify their printer's resolution in the number of pixels per inch (ppi) in the horizontal plane because it’s higher, and looks better in advertising. But all printers also have a vertical printing resolution that is mu

Re: [PyMOL] High Resolution Ray Tracing

2016-05-09 Thread James Kress
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 you