On Sun, Feb 14, 2010 at 1:18 PM, Otis Rothenberger <[email protected]>wrote:
> Hi Bob-
>
>
>> You should be able to be a bit more selective.
>>
>> delete hydrogens {atomno=3}
>>
>
> I tried that, but during a chain build, atomno is a problem because
> duplicate atomno's are created. I tried atomIndex per your above suggestion,
> but {atomIndex=3} did not seem to be an acceptable atom expression.
>
>
I was just using that as an example. Presumably you know which atom is in
need of H atoms -- yes, atomIndex is the way to go.
>
>> 4) After the use of "delete hydrogens;minimize addHydrogens," subsequent
>>> bond lengths in a growing molecule retain the length of the original atom.
>>> This was the original behavior of "minimize addHydrogens," but you fixed
>>> that.
>>>
>>>
>> say again?
>>
>>
>
> If I start with methane and build a C-C chain, I can at any point add a
> halogen followed by "minimize" producing a reasonable C-X length. The
> instant that I apply "delete hydrogens;minimize addHydrogens" that's over.
> Subsequent X is added at a C-H length.
>
OK, I'll check that tonight. Thought I had fixed that....
>
> hours, not days.
>>
>>
> You're amazing! You obviously lead several fully active lives. I'd need
> lots of naps. On this note, what's going on with Jmol and Epcot? I've
> recently moved back to Florida, and I'm taking the granddaughters to Disney
> in March. I take it that you just finished some type of Jmol project at
> Epcot??
>
Touch A Molecule -- look for the UnderWriters Laboratory display; we are
right across from that -- part of the "Nanooze" exhibit.
>
> I'll update the chemagic site with what I have on my home server and send
> you specific examples. I need to make sure that I have the most recent Jmol
> version. Is this still the 11.9.30_dev link that you sent in a previous
> email?
>
>
Pretty much. Let me have at it tonight.
> Otis
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
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--
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
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