pps -- note that ChemDoodle has its own 3D tools that don't require Jmol.
See http://web.chemdoodle.com/demos/2d-to-3d-coordinates
However, I do note that for that you have to have a subscription (for
anything at your site, that is, I think), an internet connection, and be
using a webGL-enabled browser.
On Tue, Jul 26, 2011 at 12:06 AM, Robert Hanson <[email protected]> wrote:
> 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
>
--
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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