Hi Richard,
That model is coming from Resolver. Resolver does not use MM to compute 3d
models. Basically, the steps are as follows:
1) The connection identifier (SMILES, InChI, IUPAC, etc) is broken down into
fragments called ensembles. Fixed geometries for these fragments exist in
memory.
2) The ensembles are reassembled carrying their fixed geometry into the final
SDF.
This provides fast calculation of 3d models acceptable of cheminformatic usage,
but geometries are often not consistent with MM calculations. For example, the
Resolver load of cis-2-butene produces perfect 120 degree sp2 carbon atoms.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Mar 22, 2016, at 11:11 AM, Richard Steane <richard.ste...@ntlworld.com>
> wrote:
>
>
> Hello All but Bob in particular
> Another of my less sophisticated questions:
>
> I am updating some of my files about simple biological chemicals
> http://www.biotopics.co.uk/jsmol/fattyacids.html
> <http://www.biotopics.co.uk/jsmol/fattyacids.html>
>
> Elaidic acid - a trans fatty acid - has a double bond in the middle of its
> chain.
>
> Having followed your advice and applied 'set multiplebondspacing 0.4' , I am
> happy that the double bond now displays in line with the rest
> of the chain, as I expected. Thank you.
>
> The file I am using is in fact just an edited version of the stearic acid
> file above it.
>
>
> I notice that the Wikipedia page on Elaidic acid shows 2 static images which
> are more or less straight, but
>
> the Jmol interactive image from this page:
>
> http://chemapps.stolaf.edu/jmol/jmol.php?model=O%3DC%28O%29CCCCCCC%2FC%3DC%2FCCCCCCCC
>
> <http://chemapps.stolaf.edu/jmol/jmol.php?model=O%3DC%28O%29CCCCCCC%2FC%3DC%2FCCCCCCCC>
>
> gives a molecule which droops down on either side of the double bond.
>
> Is this what is intended?
>
> Best Wishes
>
> Richard Steane
>
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