Nick Greeves wrote: > Hi Bob et al, > This looks very interesting. > Could the energy plot for rotation of a methyl group be extended to > show an interactive energy graph for any change in conformation?
The Jmol script is just driving the angle using rotateSelected and then calculating the energy. That's pretty crude -- no optimization. So I'm fairly certain that the energy barrier is way off. Right now you can't "fix" atoms -- that would be necessary to do this right, and I know I need to implement that. But the links are there. > In the past I have used QuickTime movies from Spartan to display this > but it would be much nicer to use Jmol. > e.g. Substituted cyclohexanes > http://www.chemtube3d.com/EliminationE2regioselectiveA.html > Diastereoisomer A and B links towards the foot of the page. > One way might be to perform an energy calculation on every frame of an > .xyz sequence and display the results as in Bob's energy graph. I think unless you are also offering the user the opportunity to build his/her custom molecule, it makes more sense to pre-calculate all the energies and just display them with the frame the way Hens Borkent has done. (Hens also has a builder at http://wetche.cmbi.ru.nl/organic/.) Bob > All the best > > Nick > > -- > > 3D Organic Animations http://www.chemtube3d.com > > Tel: +44 (0)151-794-3506 (3500 secretary) > > > > > On 31 Mar 2008, at 22:41, [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> wrote: > >> >> This script illustrates some very hot new capabilities of Jmol -- >> rotation of a methyl group; calculation of the energies of the >> rotatmers and display of the energy using a bar graph and echo text; >> clicking on a drawn line gets picked up as a Jmol script callback (no >> JavaScript here!) to rotate the structure to its corresponding rotamer. > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services for >just about anything Open Source. >http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor 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 ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
