I need a volunteer to help me with lipophilicity over the next couple of
days. Jmol 12.0.RC19 will have a new "MLP" option for isosurface. What I
need to know is:
-- What should be the default distance function? I see several -- 1/d, 1/(1
+ d), e^-d, e^(-d/2). Are there more? Are they all important? These four are
implemented in Jmol now, but I don't exactly see why any one would be better
than any other.
-- What is the preferred color scheme?
-- I need some comparison examples, both in the small molecule and the
biomolecule area. Mostly I'd like to see what other programs do to map a
surface with MLP data. I've tried this a bit with Chime and it just looks so
bad I can't do anything with it. And I've tried it with PyMol using a PQR
file, but I don't see how to adjust PyMol to give me different cutoffs.
(Jmol now has the pyMLP implementation of molecular lipophilic potential.)
Thanks,
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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