Bob,
Sure, add it. It's a powerful resource.
I looked at Jmol.js jmolLoadAjax_STOLAF_RCSB(). I get it now. I didn't know
you could do that.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Robert Hanson" <hans...@stolaf.edu>
Sent: Tuesday, March 15, 2011 3:54 PM
To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public
Databases
So, Otis, what I am wondering about is whether you would allow us to add
jmolLoadAjax_STOLAF_NIH
to Jmol.js. It would allow any applet (or knowledgeable user on any
applet's page) to load any of the NIH models into Jmol directly, without
need for the signed applet. You can try this yourself for the PDB. Just go
to any page on the web that uses Jmol and a relatively recent (3 years?)
version of Jmol.js, and enter on the URL line:
javascript:void(jmolLoadAjax_STOLAF_RCSB())
As I said, this hasn't been tested much with recent browsers.
Bob
On Tue, Mar 15, 2011 at 6:30 AM, Robert Hanson <hans...@stolaf.edu> wrote:
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=BSYNRY
MUTXBXSQ-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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If nature does not answer first what we want,
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-- 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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