I assume the applet. Bob Hanson can explain the details. I've not yet
written any scripts - I treat them as a black box, and make the minimum
changes to make it work.
My "SeqView"program is meant to be a help to protein engineers. The
demo for globins is at:
http://globin.bx.psu.edu/hbvar/seqview.html
The goal was to use the amino acid and position within the sequence as
parameters
It is not yet user friendly, but of use to those in the field.
I've programmed in VB6 or VB-NET, independent of Word, Excel.
One or several WebBrowser elements are placed on a VB Windows
form. Each has its Jmol contact
So far, it is a one way conversation - commands to Jmol
I've not tried VBA.
Yes, the file method is not a problem. I have to use the same method to
present my graphs as a pdf file via the Adobe ActiveX.
But in the long run, and for timing problems, it would be good to stay
in memory (the old Ram-disk is greatly missed).
Michael
On 15/03/2011 16:45, Otis Rothenberger wrote:
Michael,
OK, you definitely have my attention. Communication between Jmol and
local applications is a great idea. I have a few questions:
1) Are you doing this with the applet or the application?
2) It sounds like you are currently "talking" to Jmol with your VB
code independent of traditional applications - e.g. Excel, Word, etc.
Is that correct?
3) Have you attempted to do this with an application, say Excel, using
VBA?
From Jmol's perspective, I think I understand why the file has to be
written, but I don't see that as a big problem. I have a few other
questions, but they are in the context of a reply to Bob's note. I
think I'll post them in another email to this chain.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University Normal, IL 61790-4160
http://chemagic.org
------------------------------------------------------------------------
*From*: "Michael Marden" <michael.mar...@inserm.fr>
*Sent*: Tuesday, March 15, 2011 11:05 AM
*To*: jmol-users@lists.sourceforge.net
*Subject*: Re: [Jmol-users] Continuing Saga of Jmol Talking to Public
Databases
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
<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
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Robert M. Hanson
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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,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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