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.)
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
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
Bob, I know nothing about the basis of lipophilicity ither than having seen it a couple times in
Chime, coloring molecular surfaces.
I'll try to check tomorrow some examples in Chime and maybe in Accelrys Discovery Studio
Visualizer too (don't remember now if it offers MLP, but might be, in which case that would be
a good source and comparison).
I see this as (another) great addition to 12.0!!!
The Wikipedia page saying that Jmol was not a full alternative to Chime has its days
counted! (There was quite an argument over that sentence)