Bob--this is truly amazing! Our students just last semester were asking about docking small molecules to proteins in Jmol...this'll be interesting to explore with existing PDB structures...wonder if Jmol agrees with the crystal structures from an energetic and conformational point of view? That'd be an interesting test of Jmol's minimization algorithm, too... :-)
Cheers, Mike On Thu, May 27, 2010 at 9:30 PM, Robert Hanson <[email protected]> wrote: > I have two new demos up at > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > 137. set picking dragMinimizeMolecule -- responsive docking > With Jmol 12.0.RC15 you can move a small molecule around and watch it react > to its environment. Grab the caffeine molecule and move it toward the > protein. Holding SHIFT down allows rotation. CTRL-Z undoes an action; CTRL-Y > does a redo. > Finally I think I have a visualization for the "solvent surface"! -- Just > roll the water molecule along and see where it settles. > > > 136. set ModelKitMode > Jmol 12.0.RC15 represents a first attempt at creating a model kit option > for Jmol. Click on the magenta bar in the top left corner. > > > Give them a try! > > 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 > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Mike Evans Organic Chemistry Graduate Student Moore Group University of Illinois, Urbana-Champaign
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