sorry -- meant to respond there...
Nick - that is a perfectly good point. Obviously a 2D representation is
ambiguous with regard to conformation. So that's a limitation. I've put in
some minimal checks, but it is still going to be an issue.
Particularly with cyclohexane conformations you might get odd results as you
mention.
Bob
> On Sun, Apr 11, 2010 at 5:03 PM, Greeves, Nick
> <[email protected]>wrote:
>
>>
>> Yes, very cool and easy to use, perhaps too easy?
>>
>> My concern is the limitations of the minimisation which will lead to high
>> energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair,
>> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per
>> se but could be misleading.
>>
>> Otherwise works nicely.
>>
>>
>>
--
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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