Hello, PyMOL users!

I'm new to this list. Some may recognize me as the current principal developer of Jmol. Until recently I hadn't explored PyMOL much, mostly because I'm not myself a biochemist. For about three months now, though, Jaime Prilusky (Weizmann Institute) and I have been working on a PSE file reader for Jmol, and I think we're just about ready to roll that out, at least in a preliminary version.

A few questions:

Q: Does the availability of a way to manipulate PyMOL models on the web using Java or just HTML5 interest this crowd? Or are people more focused specifically on journal image production or stand-alone PyMOL application use?

Q: Are there people on this list who can answer fundamental PyMOL programming issues, or is that another list? I'm pretty much a autodidact, but there are some nuances that I don't understand. I don't want to waste this list's bytes if questions like "Is the second array in a scene color definition list always just a list of 1s?" are inappropriate.

Q: I also have lots of questions relating to how you go about doing things in PyMOL. (Getting a list of all defined scenes, for example.) OK to ask those here?

Q: Now that we have a pretty good handle on how PyMOL is organized and most of the basic data structures, and with all the basic modeling options reproducible in Jmol, we need more examples. More interesting CGOs than "Hello, World," examples of various specific objects such as Surface object, that sort of thing. I think I'm just about done with our current sample set of about 100 PSE files. Anyone interested in contributing PSE files to the Jmol project? Is there a repository somewhere of those?

Thanks in advance,

Bob Hanson

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900