ps -- the easiest way to load a MOL file with minimization if you know it is
in 2D format is to use the 2D filter:
load t.mol filter "2D"
This tells Jmol that the 0s in the Z coordinate are just because the file is
2D, and Jmol should try to minimize the structure with added hydrogens.
First, though, Jmol will tweak the coordinates a bit to deplanarize it in a
relatively rational way. That probably does about as well as you will be
able to do in Jmol from a 2D sketch.
Bob
On Mon, Jul 25, 2011 at 3:30 PM, Paul Pillot <
[email protected]> wrote:
> After further testing, at Angel Herraez DIY pages :
> http://biomodel.uah.es/en/DIY/ ...
> I tried all the different sketchers, and they all give the same result with
> the 2-methylbutane : an hydrogen is missing. Same goes for C n°2 and 3 for
> 2,3 diméthybutane.
>
> JMEtoJmol on Otis Rothenberger's Chemagic website displays the correct
> molecule.
>
> -Paul
>
>
>
>
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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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