It was a bug with the H atom addition. See fixed:
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Mon, Jan 3, 2011 at 8:18 AM, Otis Rothenberger <[email protected]>wrote:
> Bob,
>
> The quickest way to see this is to load PCl5 from Resolver via SMILES and
> then replace one of the transaxial bonds with a methyl. In this case, you
> can pull the hydrogen's out of what I'm calling back bonding with minimize.
> In some cases, they are hopelessly stuck - i.e actually coincident with the
> central atom.
>
> Tom is working on isomer construct/compare problems, so the bond elongation
> trick is working. Again, I assume this elongation prevents the coincidence
> of H and central atom.
>
>
>
> Otis
>
> --
> Otis Rothenberger
> Department of Chemistry
> Illinois State University Normal, IL 61790-4160
> http://chemagic.org
>
> ------------------------------
> *From*: "Robert Hanson" <[email protected]>
> *Sent*: Monday, January 03, 2011 8:08 AM
> *To*: [email protected]
> *Subject*: Re: Partial Wrap Up of the Coordination Issue
>
>
> I think perhaps the backbonding is fixable. What's an example?
>
> On Sun, Jan 2, 2011 at 9:28 PM, Otis Rothenberger
> <[email protected]>wrote:
>
>> Bob,
>>
>> Tom is headed off to Columbia, South America soon, and he wanted to start
>> working on some coordination model exercises before he leaves. Actually, he
>> was having a cow about the current state of my coordination scripting in the
>> model kit. I cleaned things up so that the kit is now functional in this
>> sandbox. To do this, I used some work arounds, which I know you don't like.
>> So this is my confession, but I'll work on cleaning it up. The following is
>> our message to users when coordination templates are loaded:
>>
>> "Note: The central atom in this model is xenon. It has been arbitrarily
>> selected as a generic central atom. Retaining this generic central atom will
>> allow editing ligands without altering central atom geometry."
>>
>> The spirit of the above statement is not really a work around, and I can
>> clean it up to work with central atoms in general. Picking Xe as a generic
>> central atom was just a convenience to get operational. I can generalize
>> this approach. Here's the work around, however:
>>
>> In all of this, the hydrogen atom back bonding that I referred to
>> previously is a problem. It occurs when ligands are at 180 degree angle. A
>> fix (oops work around) is to elongate all of the ligand bonds on the
>> original template. I assume what's going on here is that newly added H atoms
>> are too far removed from the central atom for back bonding.
>>
>> I know how to implement the generalization of the central atom (as opposed
>> to using only Xe), but I have no idea about the back bonding issue.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> Department of Chemistry
>> Illinois State University Normal, IL 61790-4160
>> http://chemagic.org
>
>
>
>
> --
> 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
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