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
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
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it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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