Otis, I'm still having problems with deleting and adding hydrogens. I'll
work on this later tonight and get back to you.
Bob
On Mon, Feb 15, 2010 at 2:53 PM, Robert Hanson <[email protected]> wrote:
> Otis wrote:
>
> I'm still having problems with timing on minimize. If I call this as a part
> of a single script, I randomly get hydrogen atoms that are not connected.
>
> I'll need to see that in action. One thing I just this morning fixed was a
> problem that deleted atoms could in principle show up later, and that could
> be part of this.
> The "connect" command may or may not reconnect them, depending on how far
> they drifted during the minimize. All of this goes away if a separate
> minimize command is given via a link after the rest of the substitution
> script runs.
>
> I need exact histories if possible. What exact commands were given?
>
>
>
>> One solution is to allow the user to elect "minimize" via a link after the
>> molecule is built or at various stages during the build. Delete of specific
>> hydrogens rather than all may also help resolve the problem.
>>
>
> The solution is to find the bug in Jmol, not work around it.
>
>
>>
>> Actually, a separate minimize link makes sense for another reason. The
>> minimize delay is really disruptive during model building.
>>
>>
> Yes, I think separate minimization does make sense. Note that you do not
> have to display the minimization in progress. That's just for fun.
>
> Bob
>
>
>> Otis
>>
>> --
>> Otis Rothenberger
>> http://chemagic.org
>>
>>
>> ------------------------------------------------------------------------------
>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
>> http://p.sf.net/sfu/solaris-dev2dev
>> _______________________________________________
>> 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
>
--
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
------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
