Happy to report that Robert Lancashire and I have successfully integrated
the Jmol http://jmol.sourceforge.net/ and JSpecView
http://jspecview.sourceforge.net/ projects. Here's how it works:
Application: see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol.jar
Jmol now incorporates JSpecView as one of its modules. This allows the user
to open up a JSpecView window. (See the Tools...JSpecView menu item.) In
addition, if a model is loaded that is of a new type -- a JCAMP-DX file
with added ##$Models and ##$Peaks records, then clicking on atoms in the
Jmol window will automatically call up and highlight the associated C or H
NMR spectrum peaks, and clicking on a peak in the spectrum will highlight
the atoms in Jmol. (This functionality is turned on using the command SYNC
ON). Using the RIGHT_ARROW and LEFT_ARROW keys on the spectrum will quickly
jump from one IR band to another, showing the vibration in the model, or
one NMR signal to another, highlighting the atoms involved.
Applet: see
http://chemapps.stolaf.edu/jmol/docs/examples-12/jspecview/test1.html
The Jmol applet can now synchronize with the JSpecView applet on a page.
This allows displaying of spectra and model at the same time, with the same
sort of coordinated clicking as in the application. It's just a JavaScript
connection (which you can adapt as you see fit) rather than a direct Java
connection.
Hopefully this will be of interest to some Jmol users. Of course, it all
hinges on having spectra files that have both model information and peak
assignment information in them. That's new, and we think we have a pretty
good scheme for making it relatively easy to set up. Basically what we are
doing is embedding one or more MOL files in the JCAMP-DX file and then
pointing to them in a simple way to define peaks. If you take a look in
http://chemapps.stolaf.edu/jmol/docs/examples-12/jspecview you can see a
few examples. One thing you may notice there is that we use MOL files (but
really it could be any nonbinary format that Jmol reads) for the NMR
correlations and XYZVIB files for IR data. Bonding for the XYZVIB file is
provided by a "base model" which is also a MOL file.
So this all works.
What we would like to do now is figure out a simple way to help users
quickly correlate peaks with atoms or vibfations. This is probably a
WebExport sort of functionality, I don't exactly know. All ideas are
welcome. The output would be a JCAMP-DX file. Looking for volunteers for
that. Should be a publication, I would think....
In addition, if anyone already has correlated data -- NMR spectra in JDX
format with known mapping to atoms of a specific MOL file -- we'd like to
know about that. Does anybody have anything like that? We're also looking
for net-based applications that could, for example, be sent a MOL file and
have a simulated HNMR or CNMR spectrum returned, packaged in JDX format,
with the incorporated ##$Models and ##$Peaks records. Any suggestions?
Bob Hanson
--
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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