Hi Bob,
Is there a way I can access this type of JavaScript functionality from my Java
app that embeds Jmol and talks to it through the JmolViewer?
JmolViewer jmolViewer = JmolViewer.allocateViewer(this, new
SmarterJmolAdapter(), null, null, null, null, null);
Thanks,
--Chuck
On Mar 15, 2011, at 3:54 PM, Robert Hanson wrote:
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<mailto: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<mailto: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<http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=%27InChIKey=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<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: <tel:507-786-3107> 507-786-3107<tel: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<tel: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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