Bob,
Well, OK, but...
2,4-Dimethylpenta-2,3-diene
(winking smiley face)
It turns out the Jmoll's implementation of MMFF94 doen't get
2,4-Dimethylpenta-2,3-diene out of the above linear minimum - not sure about
UFF. I have to check the docs to see how you turn UFF on. I forget.
Drag/sculpt moves you toward the correct picture, but even there you're
fighting other minimums.
Otis
Sent from my iPad
> On Dec 7, 2015, at 7:01 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> the PubChem 3-D conformer model for a chemical structure represents all
> possible “biologically-relevant conformations that the molecule may have”.
>
> Well, not in this case. So then it's just a bug in PubChem. Obviously allene
> will not have a flat conformation in a biological system.
>
> Bob
>
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