ps preliminary specs are at
https://docs.google.com/document/d/16Ht5baVsDogiJlZr7IvugM0sE5r22rLmFw5fVHS
Bob
On Wed, Feb 15, 2012 at 2:36 PM, Robert Hanson <[email protected]> wrote:
> 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
>
--
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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