Bob-
>> evalRasmol("{atomIndex=" + atomIndex + "}.element = '" + buildAtom
>> + "';");
>>
>> evalRasmol("set useMinimizationThread false;echo working...;delete
>> hydrogens;minimize addHydrogens;wireframe 0.15; spacefill 23%;boundbox
>> {*};centerat boundbox;minimize steps 100;");
>>
>> setTimeout("doUFF()",2000)
>>
>> The above modification of my code is pretty much the result of trial and
>> error. I'm not sure I understand why, but the code must be just so. I cannot
>> simply do a longer minimize in the second evalRasmol function. Further, even
>> though the minimize is the last command, the "set useMinimizationThread
>> false" is required.
>>
>
>
>
> ...or what happens?
>
On a conversion of methane to methylamine, the coincident or close to
coincident hydrogens will not resolve unless the "set useMinimizationThread
false" is present. This may be related to my whole timing problem with
minimize (see below).
>
>
>>
> Nevertheless, it works with your applet modifications. Some specific
>> points:
>>
>> 1) Formaldehyde to imine via N substitution for O still produces the
>> strange H insertion, but the above code corrects this.
>>
>
> not sure which code you are referring to -- mine or yours.
>
My mistake.This is now OK
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.
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.
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.
Actually, a separate minimize link makes sense for another reason. The
minimize delay is really disruptive during model building.
Otis
--
Otis Rothenberger
http://chemagic.org
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