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> 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>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
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> 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
>
--
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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