Otis, if you think it would be valuable, we could look into reading the
stereochemistry of bonds and at least shifting a whole branch up or down an
angstrom in the Z coordinate based on that. wouldn't be perfect, but it
might not be that hard, either.
As I started to do this, I realize that the JME reader is totally
nonfunctional. I'm adding stereochemical reading, and it seems to work OK,
but there is still a problem with the addhydrogens business. WIll fix....
On Fri, Apr 9, 2010 at 1:28 PM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> Bill,
>
> I'm passing molfiles from JME. Actually, the SMILES is also passed in
> the molfile (Name Position), but its the molfile that's rendered.
>
> The JME string might be worth a try. While the information is still 2D
> only, we have found that you can give UFF minimization good starts and
> bad starts based on the original 2D drawing. It's important to note that
> Jmol ignores stereo bonds from JME - only 2D info passed. Interestingly,
> it will pass formal charge information in the molfile, but the atom is
> not registered in Jmol as having the formal charge - i.e. the charges
> are only printed on the model.
>
> Otis
>
> On 4/9/2010 1:07 PM, william reusch 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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> >
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
> ------------------------------------------------------------------------------
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> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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