On Thu, Jan 14, 2010 at 1:07 PM, Grossman, Robert B <robert.gross...@uky.edu
> wrote:
> (1) Display H atoms. If I load a structure that does not show H atoms, it
> would be nice to have Jmol calculate their positions and display them. I
> know it must know that they are there, because when I loaded a structure
> with a planar C the the center of an isopropyl group, then minimized the
> structure, it converted the C to tetrahedral. (I guess it's possible you
> have this feature, but I'm not able to find it.)
>
Jmol doesn't know they are there. The UFF calculation is simply optimizing
the single-bond C-framework. If the problem can be better defined, we might
be able to do something about it. Certainly would be a good trick. Do you
have the bonding already -- double, triple? One problem, for example, is:
C -C-O
is that CH3CH2OH? CH2CH2OH? CH2C=O? CH3CHO? If the bonding is there, then we
are ok; if it is not, then
But if you have double bonds, it's easy. Send me a file.
Bob
--
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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