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
http://www.stolaf.edu/people/hansonr
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
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