Bob,
First, AAARGH! Finally.
Here’s what messes up [n = {*}[0].molecule;show n] in Jmol - Otis.htm and
Test2.htm
PubChem provides SDF's with partial charges and without partial charges.
Actually, they are always there, but some are listed
> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
0
If the PubChem file actually lists non-zero charges, then cutting the resulting
molecule up in Jmol makes [n = {*}[0].molecule;show n] behave erratically.
I load by default from PubChem, and a McLafferty Rearrangement model kit
problem using hexanal that I was setting up started this whole email chain with
the mf problems. I just kept working with PubChem hexanal while I was trying to
find the “funky” behavior on my page. It was just dumb luck that I noticed the
PubChem relationship.
OK, now that I can use n = {*}[0].molecule, I need to get the mf array over to
JavaScript. What’s the best route - message callback?
Finally, it seems to me that if CH2 is in the Jmol window, then a simple
extraction of mf should be CH2 - not CH4. I’m just saying. This, of course, is
a small molecule guy’s opinion!
Otis
--
Otis Rothenberger
[email protected]
http://chemagic.org
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