From: Nick G. <ngr...@li...> - 2008-03-31 22:05:20
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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? 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. 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, jmo...@li... 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. |
From: Bob H. <ha...@st...> - 2008-03-31 23:54:36
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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, jmo...@li... > <mailto:jmo...@li...> 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 >Jmo...@li... >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 |