I think you should always be able to know where the atom is to go. If it
were me, I would always do atom replacement, so when, say, I click on an H
atom, it becomes a CH3. Isn't that the way Spartan does it? I would just
follow their lead on that. No need to reinvent the wheel here.
Bob
On Fri, Feb 19, 2010 at 11:21 AM, Otis Rothenberger <[email protected]>wrote:
> Thanks Bob and Rolf.
>
> {*}.length to get the atomIndex of the appended atom makes the embarrassing
> astatine trick go away. It also has some general utility.
>
> Bob, putting the appended atom anywhere in the reach of other atoms seems
> to always get it mired in a web of strange bonds after "minimize
> addHydrogens." This happens even if I omit the delete hydrogens.
>
> I'm also not sure where I want the appended atom in the general case - some
> offfset from the clicked atom's coordinates? What I'm doing as an
> alternative is placing the appended atom outside the reach of other atoms
> and then letting minimize sort it out.
>
> Rolf, I'll pursue the zoom suggestions that you made. The problem is that
> zoom 100 seems to be redefined by the absurdly long bond that I'm forming.
> Your suggestion may allow me to redefine it again after the minimization.
>
> Writing this just gave me a thought. I wonder if the appended carbon atom
> is still being viewed with astatine's radius. That might explain the web of
> strange bonds.
>
> Whatever the situation, I have some direction now. Thanks for the help.
>
>
> 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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