Bob,
Yes!
I don't have Jmol 12.0 downloaded yet, but I'll get it now. Where are
you "seeing" the stereo bonds. I don't see any stereo information in the
molfile (other than the SMILES in the header) or the jme string. Are you
reading this from the SMILES?
Once I get this set up, Tom will be playing with it endlessly, so you
should get some feedback from our end.
Thanks for the work on this.
Otis
On 4/10/2010 6:41 PM, Robert Hanson wrote:
Hey, check this out:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
124. JME reader reads stereochemistry and automatically turns 2D
to 3D with addition of H atoms
/ The JME format is a two-dimensional file format that is easy to
generate <http://www.molinspiration.com/jme/doc/jme_ex1.html> but not
easily adapted to 3D. Jmol 12.0.RC5 adds the automatic addition of H
atoms and transformation of simple JME structures (including
stereochemistry) to 3D. The transfer is not perfect, and it may take
some testing to get this right./
Bob
On Sat, Apr 10, 2010 at 4:22 PM, Robert Hanson <hans...@stolaf.edu
<mailto:hans...@stolaf.edu>> wrote:
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 <mailto: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 <http://chemagic.com>
------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find
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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
--
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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Otis Rothenberger
chemagic.com
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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