Bob,
I installed /Jmol 12.0.RC5/ on the chemagic server and set the JME
transfer code in the model kit for the JME string. In playing with the
new set-up, I did not see one error in stereo rendering of non-cyclic
systems. Structures drawn in the JME editor are processed as follows:
1) If there are stereo bonds in the structure, then the JME string is
passed to Jmol for rendering, hydrogen addition, and minimization.
2) If the unique SMILES of a structure without stereo bonds is on our
poor rendering list (currently 22 small molecules), then the load is
diverted to a molfile optimized, if appropriate, for the most stable
isomer and conformation.
3) All other structures are passed to Jmol as the JME string via route 1.
By way of example, ambiguous 1,2-dimethylcyclohexane is on our poor
rendering list. It travels route 2 to load the diequatorial chair from a
file. On the other hand, 1,2-dimethylcyclohexane drawn as trans with
stereo bonds will travel route 1 with, it turns out, pretty good results.
Otis
On 4/10/2010 6:41 PM, Robert Hanson wrote:
Hey, check this out:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
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Otis Rothenberger
chemagic.com
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