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
------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
