Isn't that fun? I'll set up a little JME reader for that new.htm page next.
It's the JME string. Previous 11.9 versions won't work because I
inadvertently broke the JME reader and never thought to test it because it
seemed, well, so useless before. But now I think it's pretty neat!.
The JME string lists up and down bond orders as -1 and -2, respectively. I'm
just passing those one to Jmol model loader, and when it sees those it takes
the pair of atoms, determines the branch leading from forward, and pushes
all atoms "in front" up one angstrom. Simple enough of an idea. Won't work
with stereochemistry indicated in rings (such as norbornane), so let's see
how it goes.
Bob
On Sat, Apr 10, 2010 at 6:31 PM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> 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> 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!
>>> >>
>>> >>
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> > 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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>>> > _______________________________________________
>>> > Jmol-users mailing list
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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.
>>> 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
>>>
>>
>>
>>
>> --
>> 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
>
>
> ------------------------------------------------------------------------------
> 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
> listjmol-us...@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> --
> Otis Rothenbergerchemagic.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.
> 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
>
>
--
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
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