[ssml] About Pymol

Kevin Karplus karplus at soe.ucsc.edu
Mon Jun 6 12:29:06 EDT 2005

I'm afraid my problems with Pymol were more basic than trackball vs
mouse---it took me half an hour to disover that I had to type <escape>
to get the picture of the molecule on my screen rather than just text.
Why Pymol has two windows, then insists on putting all the text in the
graphics window is a mystery.

I still haven't figured out how to display multiple models from a
single PDB file in Pymol.  Changing display styles for pieces of a
protein seems very awkward.

I plan to spend some time this summer learning how to produce pictures
with Pymol, and modifying the latest SAM server so that it produces
Pymol scripts as well as rasmol ones.  The ray-traced Pymol pictures
are bit prettier than Rasmol's pictures, but the user interface seems
even harder to learn than Rasmol's.  It is clear that one *has* to
read a tutorial or user manual, as nothing is intuitive. (Having the
"help" command hide the graphics was *not* very helpful.)

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Affiliations for identification only.

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