Brilliant! Wow. Absolutely. Jmol creates a SMILES string, passes it to NIH, and NIH does the 2D->3D conversion way better than Jmol ever could.

The only catch is that you won't be able to get specific conformations. So you could be surprised by the return if, say, you had a twist boat and expected a minor tweak of that. You'll get a chair instead. And possibly the flipped chair, at that.


On Sun, Aug 29, 2010 at 9:01 PM, Otis Rothenberger <> wrote:

 Jmol creates SMILES directly from an evolving model kit model. In the latter case, querying the Resolver with a Jmol SMILES generated from a model with a just so/so geometry gives a Jmol applet based application the "feel" of having a native high end molecular computation package. A single click takes the Jmol model and "NIH optimizes" it. While I'm using server side scripting to make this seamless, my assumption is that the same seamless connection would be possible with the signed applet. Am I correct on this Bob?


Otis Rothenberger

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