Otis, I think a really simple and fast way to generate a structure would be
to allow clicking on H atoms to sprout CH3 (NH2 or OH or Cl, depending upon
the selected atom choice). If possible, clicking should not allow violation
of the octet rule for C, N, or O.
On Fri, Apr 9, 2010 at 12:07 PM, william reusch <whreu...@msu.edu> wrote:
> Otis,
>
> Are you transferring the JME structure as a Smiles string or as a JME
> string. The latter has more information in it.
>
> Bill
>
>
> Otis Rothenberger wrote:
> > Bill,
> >
> > Thanks for the comments. The 2D to 3D translation is an ongoing problem
> > for us. The JME editor is light weight and it can be embedded directly
> > in the application, but it passes only 2D information to Jmol. Jmol
> > tries to sort this out with the UFF minimization. With really simple
> > molecules this works, but there are serious limitations. We actually
> > have two alternative options, and we need to discuss this in the users
> > manual, a current high priority!
> >
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
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it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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