Speaking of public databases, this might be a time to test the facility that
has been in Jmol for quite some time -- the ability of the UNSIGNED applet
to access remote files via a JavaScript interface. I don't think anyone has
capitalized on this, but there is a St. Olaf server that is built into
Jmol.js.
<JavaScript_here>
jmolLoadAjax_STOLAF_RCSB
</JavaScript_here>
Could we adapt this, Otis, to get small molecules into any applet?
Bob
On Mon, Mar 14, 2011 at 10:39 PM, Otis Rothenberger
<osrot...@chemagic.com>wrote:
> All-
>
> Chemical Entities of Biological Interest (ChEBI) is dictionary of small
> molecular entities. While it understands SMILES, it does not have Jmol's
> ability to FIND SMILES. Nevertheless, one can query the dictionary with an
> InChiKey. With the help of NIH/NCI Resolver, therefore, a Jmol model can be
> used to directly query the dictionary:
>
>
> http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N
> '
>
> with Resolver making the SMILES to InChiKey translation.
>
> ChERBI is a user driven database that currently contains 18000 compounds. A
> brief discussion of ChEBI is here:
>
> http://precedings.nature.com/documents/3525/version/1
>
> From a teaching perspective, this attracted my attention because it is a
> nice way to include bioinformatics into an instructional setting under the
> Jmol umbrella. While there are query accessible molfiles available via
> ChERBI, this is not the main point. Resolver and PubChem are much better
> general sources. The main point is that with one click in Jmol make the
> query, "Is the small molecule in my Jmol window of biological interest?" I
> have not yet hooked the CheMagic model kit to this site, but I expect to do
> so sometime this week.
>
> Otis
>
> --
> Otis Rothenberger
> Department of Chemistry
> Illinois State University Normal, IL 61790-4160
> http://chemagic.org
>
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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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