Two items concerning communication with Jmol caught my attention.
this one (Continuing Saga of Jmol Talking to Public Databases)
and "Command line communication with the Jmol application?"
I'm not sure if it is really relevant to the method that I'm using.
I'm using visual basic (VB) as a front end, and Jmol shows up within a
browser (within a VB window).
So I can do all my set-up, calculations etc, and then send commands to Jmol
Bob Hansen helped me set this up, using the Jmol.js and JmolApplet.jar
files.
The VB program writes a text file to disk that contains the command.
Jmol is waiting and reads it back.
So essentially I continuously pump commands to modify the molecule being
presented.
I would prefer a way to avoid the round to the hard disk, but it seems
to work well.
As Jmol is now mature, it would be good to consider communication with
other programs.
Michael Marden
INSERM, University Paris 11, France
On 15/03/2011 12:30, Robert Hanson 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
<[email protected] <mailto:[email protected]>> 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
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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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