Otis, send me a few examples. Then we'll just make a list and go through it.
Terminal alkenes should be OK now -- at least if only the terminal carbon is
missing groups. (2-methyl-1-butene should work, for example) So we just need
to keep identifying problem cases and work through those. Shouldn't be a
long list. Please check imines as well as terminal alkenes. Make sure you
use the latest -- I took ethene, ripped off two hydrogens, and then put them
back on with calculate hydrogens, and it seemed to work ok.
Bob
On Sun, Feb 14, 2010 at 10:06 AM, Otis Rothenberger <[email protected]>wrote:
> Bob-
>
> The command sequence "delete hydrogens;minimize addHydrogens" is very
> useful in cleaning up edited structures. I continue to have problems
> (11.9.30_dev) in certain situations, however:
>
> 1) Superimposition of hydrogen atoms on a terminal alkene - minimize
> unresolvable.
> 2) Near superimposition of hydrogen atoms in a nitrogen atom - minimize
> resolvable.
>
> For individual atom changes, I'm now using the following JavaScript:
>
> evalRasmol("{atomIndex=" + atomIndex + "}.element = '" + buildAtom
> + "';");
> evalRasmol("minimize addHydrogens;wireframe 0.15; spacefill
> 23%;boundbox {*};centerat boundbox;");
>
> The JavaScript variables "atomIndex" and "buildAtom" are determined by user
> click.
>
> Using the above, "minimize addHydrogens" has at least one problem when used
> independent of "delete hydrogens:"
>
> 3) Weird addition of some hydrogen atoms when added back into the molecule
> - N-H of C=N, for example (attached pic).
>
> Visually, it looks neat if I tack a "delete hydrogens;minimize
> addHydrogens" on each edit, particularly if the substituted atom has too
> many hydrogen atoms. But there is another problem with "delete
> hydrogens;minimize addHydrogens:"
>
> 4) After the use of "delete hydrogens;minimize addHydrogens," subsequent
> bond lengths in a growing molecule retain the length of the original atom.
> This was the original behavior of "minimize addHydrogens," but you fixed
> that.
>
> I'm working on kludges for these issues because I want to keep an evolving
> working Jmol model page on our site. We're trying to get high school
> chemistry students (and teachers) excited about using Jmol, and a working
> model page continues to attract attention. Obviously, true fixes are better
> than kludges, but that will take time.
>
> 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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