Nick Greeves wrote:
> Is there a command which will generate multiple bond types (even just
> double would be a start) from a structure that lacks such info e.g.
> .xyz ?
>
It's
select {*} // maybe
connect aromatic modify
calculate aromatic
The idea is that aromatic systems are conjugated systems, and Jmol knows
how to follow the conjugated single/double sets in a clever way to
always produce the best set of double bonds (if there is one).
You can actually select all the atoms, but I don't recommend it, because
that might throw off minimization. What I was doing for caffeine was:
select connected(2) or connected(3) or oxygen and connected(1)
At least that was good enough for caffeine. A general solution would be
somewhat more specific -- connected(3) and (not nitrogen or nitrogen and
connected({oxygen})) -- something like that. You want to include the
carbonyls even though they are not technically aromatic.
Bob
> I've looked at Connect Calculate and Set autobond ON but none seem to
> do the job.
> connect aromatic auto does the job for aromatic compounds but I've
> found nothing else.
>
> What I'm looking for is automatic recognition of carbonyl groups,
> alkenes etc. Up to now we have been putting them in by hand and I
> notice that MacMolPlt can do it (not always perfectly).
>
> All the best
>
> Nick
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
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If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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