On Wed, Sep 16, 2015 at 9:30 AM, Otis Rothenberger <osrot...@chemagic.com>
wrote:
> Bob,
>
> I do not consider this a work around because it’s not Jmol’s fault! For
> example, ammonia and pyrrole are both (nitrogen and connected(3)).
>
>
I would use SMARTS searching. It is very powerful and can distinguish
anything.
$ load $pyrrole
$ select within(smarts,"{[nD3]}")
*1 átomos seleccionados*
$ load $ammonia
$ select within(smarts,"{[nX3]}")
*0 átomos seleccionados*$ select within(smarts,"{[NX3]}")
*1 átomos seleccionados*$ load $imine
$ select within(smarts,"{[NX3]}")
0 átomos seleccionados
$ select within(smarts,"{[NX2]}")
1 átomos seleccionados
Question:
>
> For cases where I had to empirically discover the correct “p-xyz” or
> “sp#-abcd” I may run into problems with my scripts that are related to how
> the model was constructed. In other words, starting with methane, MOLECULAR
> hybrid-abcd and p-xyz might get screwed up. Is this a correct assumption?
>
It's a bit difficult to generalize, probably.
You can also direct LCAO orbitals to specific atoms.
load $methane
$ p = {h2}.xyz - {c1}.xyz
$ LcaoCartoon ID "lcao1" center @1 lobe @{plane(p.x, p.y, p.z, 0.7)}
atomIndex 0
I'm not sure that is documented, but it is in the state that way.
>
>
> Question:
>
> If the answer to the above is “yes,” then would forcing the user to use
> JME for constructing the initial model prior to LCAO solve this problem?
>
> As an aside, I should have added this feature a long time ago. I don’t
> know how it escaped me.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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