[PyMOL] Capturing a selection with a plugin

2004-08-30 Thread Michael George Lerner
Hi, With the old wizard interface, I could capture selection actions with the do_select method. Is there a similary way with the Plugins? (I'm willing to write more code, I just don't know quite where to start.) Thanks, -michael -- This isn't a democracy;|_ |Michael L

[PyMOL] Print Distances

2004-08-30 Thread Bob Havlin
Is it possible to get pymol to simply print a list of selected distances from a command such as: distance foo = (name P), (chain B and name ca), 8 This command shows the distances nicely in the gui, but I would like a table of the atoms and their respective distances. Thanks, Bob

[PyMOL] Image DPI

2004-08-30 Thread Christopher Colbert
Hi PyMOL-users, I have taken a look into the archives and FAQs about making 300dpi images. It seems straight forward on the surface, image size in inches * 300dpi gives the number you put into the ray command. However, there is mention of correcting for aspect ratio, which is defined by the viewp

RE: [PyMOL] PyMOL tutorial (moved and slightly updated)

2004-08-30 Thread Warren DeLano
> Why do you think pymol cannot be sold? The copyright license > does not seem to imply this[1], and such a restriction would > render pymol not Open Source. > Warren, can you tell us what you think on this? Michael & Carly, Yes, in my world, open-source means available to all people and for

RE: [PyMOL] 3d plotting in pymol

2004-08-30 Thread Amit Chourasia
Tsjerk, Hope you are doing fine. I was toying with your graph.py script. I am trying to mod it to generate solid cube.( display triangles instead of lines) Could you toss an example how to add triangle inside your graph.py? I could not find details in the docs. It appears pymol needs normals for a

[PyMOL] Secondary structure and surface

2004-08-30 Thread Alex W. Smith
Greetings PyMolers: I have a couple of questions. I am working on some figures and have found, at least for my particular protein, the DSS in PyMol does a better job with secondary structure assignments than DSSP. I have checked the assignments against the map and model in O. Is there any