This is kind of cool. Jmol 14.2.0 will allow side-chain minimization. What
you do is to use the "model kit" icon (methane molecule) and from the upper
left menu under atoms, select "drag-minimize molecule (docking)"
Then grab a protein side chain and give it a yank.
It's advisable to use
set pdbAddHydrogens
prior to loading so you get full protonation, because otherwise it can
easily flip a threonine or isoleucine C-beta stereocenter.
The version that has this now is
http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.17/Jmol-14.1.17_2014.06.12-binary.zip/download
in case you want to play.
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
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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