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
<<attachment: jmolPic.jpg>>
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