OK, Otis. We are making progress. With this next revision, imines should
work, and there is the possibility that cumulenes will work. The
qualification is that if the starting cumulene has no hydrogens at all (for
example, just C=C=C), Jmol won't be able to handle it, because it adds the H
atoms only after doing the full calculation, and in the case of cumulenes
you need to have one end of the cumulene hydrogens in place in order to
orient the other end. Still thinking about that one...
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Bob
On Mon, Feb 15, 2010 at 11:03 PM, Otis Rothenberger <[email protected]>wrote:
> Bob-
>
> All right! That did it. I think there was a typo in your URL, but I think I
> got the correct file.
>
> I think it looks pretty slick in action, including the bond order changes.
>
> I'm now deleting only the hydrogen atoms on the affected substitution
> atoms, and this brought back a problem. N atom substitution for the O in
> formaldehyde once again produces the backward imine (earlier jpeg). Now,
> however, a delete all hydrogens followed by minimize addHydrogens corrects
> this.
>
> Expressed in JavaScript I now have:
>
>
> evalRasmol("{atomIndex=" + atomIndex + "}.element = '" + buildAtom
> + "';");
> evalRasmol("select hydrogen and connected({atomIndex=" + atomIndex
> + "});delete selected;");
> evalRasmol("minimize addHydrogens;");
> evalRasmol("select *;wireframe 0.15; spacefill 23%;boundbox
> {*};centerat boundbox;");
> evalRasmol("set minimizationRefresh false");
> evalRasmol("minimize steps 100;");
>
> As I said above, this does produce a backward imine.
>
> I guess I use eval because of the concatenation and the analogy to
> JavaScript eval. The evalRasmol dates back to this project starting years
> ago in Chime.
>
> I'm going to spend the next couple of hours cleaning up the mess that my
> .js pages have become and then put the page on the chemagic server.
>
> Otis
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
> ------------------------------------------------------------------------------
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>
--
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
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