Ah, good deductive work. Actually, it was a problem in the two modes of H
addition. The rule is supposed to be:
If you just use
calculate hydrogens
Jmol will respect any atom that already has hydrogens on it and not add any
more, under the presumption that perhaps you want it that way.
If you use
calculate hydrogens {someAtomExpression}
then Jmol will fill out all atoms in that set to it's understanding of how
many hydrogens should be on that atom.
Bob
On Fri, Feb 26, 2010 at 7:50 PM, Otis Rothenberger <[email protected]>wrote:
> Bob-
>
> OK, I think I see something consistent in the delete problem now:
>
> Delete followed by "minimize addHydrogens" works if the deleted hydrogen is
> the only hydrogen on the multivalent atom. In every other case I look at, I
> see it failing:
>
>
> I'll use methanol to exemplify this, but I think it's pretty general:
>
> 1) Delete the alcohol H, and you can put it back on.
> 2) Delete 1 methyl H, and you cannot put it back on.
> 3) Delete 2nd methyl H, and you cannot put it (or the first deleted) back
> on.
> 4) Delete final methyl H, and you can put them all back on.
>
> Otis
>
>
> On Fri, Feb 26, 2010 at 2:50 PM, Otis Rothenberger <[email protected]>wrote:
>
>> Bob-
>>
>> Using your approach, picking deletes an H on propane. But minimize
>> addHydrogens does not add it back. I'm thinking maybe I have the wrong Jmol
>> version. I'm using 11.9.30_dev 2010-02-12 12:26. Is this the wong version?
>>
>> The two minimization steps simply reflect the fact that I forgot
>> "calculate hydrogens" was an option. I also need to clean the multi-step
>> calls to jmoScript(). That goes back to when I thought I had timing
>> problems. I was playing with delays in various parts of the script, and
>> breaking things apart was just a convenience.
>>
>> evalRasol is history! How about sortOutOtisConvolutedWayOfDoingThings()
>> for the replacement. :) I guess I'll just use processJmol(). Actually, the
>> function processes Jmol and JavaScipt entered in the page's text field.
>>
>>
>> Otis
>>
>>
>> --
>> Otis Rothenberger
>> http://chemagic.org
>>
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
> ------------------------------------------------------------------------------
> 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
> [email protected]
> 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
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
