Well, what do you know? Eric Martz is going to go nuts...
Jmol now does docking with automatic minimization.
This is simply:
set picking dragMinimizeMolecule
Then, whenever you let go of a dragged a molecule, it minimizes automatically. Holding SHIFT done does a molecular rotation.
In the application, the easiest way to invoke this is via the model kit, which is a new tool bar item in the middle of the tool bar. This brings up a new menu in the top left corner that guides you through the options.
Of course, the caveat is that the Universal Force Field is pretty simple and not at all accurate in terms of real energy, but still, it's awfully fun to see caffeine bounce off an enzyme!
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