On Tue, Mar 15, 2011 at 11:56 AM, Otis Rothenberger
<osrot...@chemagic.com>wrote:
> Bob,
>
> I think we still run into the cross domain security violation with the St
> Olaf server.
>
>
Nope - no cross-domain server issues with JavaScript servers. Just HTML
servers. Could be odd browser issues -- that's what needs testing.
> Some Continued Questions Related to Michael's Note:
>
> 1) Do you know if the applet running locally with a local file address is
> subject to disk writing restrictions?
>
Certainly it needs the signed browser. Newer browsers have imposed
additional file-directory restrictions for reading files, but not writing.
It's just a file dialog that pops up.
>
>
> *From*: "Robert Hanson" <hans...@stolaf.edu>
> *Sent*: Tuesday, March 15, 2011 7:30 AM
> *To*: osrot...@chemagic.com, jmol-users@lists.sourceforge.net
>
> *Subject*: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public
> Databases
>
>
> 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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> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
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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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