It's a structural database, so it will access MOL files, but it's more than that, because we have the internal coordinates--bond angles and distances, not z-matrix--in JavaScript already for over 500 molecules. What's interesting is the plan to incorporate vibrational normal modes into the data. In the past we would have had to create and save animations for every normal mode of every structure as static files on the server--I would imagine on the order of 4000 files.
But, thanks VERY MUCH to Miguel, what we are going to be able to do is create the vibrational mode information on the fly with JavaScript and use the loadInLine option to pop up a new window with the vibrational animations. So there will be no "normal mode" files whatsoever.
Before we develop this, I'd appreciate someone showing me what that vibrational jmol capability is--but I'm going to have the student work out the animations anyway, because I think it will be a very good experience for him. Are there examples of vibrational display in jmol somewhere?
Bob Hanson
Miguel wrote:
Bob wrote:
[snip] But some will imagine a reaction sequence such as that Diels-Alder reaction, where bonds change. ... I guess what I'm arguing for is a flexibility in bonding but not necessarily in number of atoms.
Jmol will *always* prefer to take the bonds from the file and faithfully render what is in the file.
Here's a question: what happens if, upon an animFrameCallback you send a script to the target model?
Probably something will break ... and there is a good chance that the browser will break before Jmol breaks.
1. Could one then create an animation that shows atoms, bonds, etc. differently from frame to frame that way--even change their colors? Has anyone tried this?
Yes. It works fine today.
2. Could such a script be incorporated somehow right into the CML or MOL description (say, for instance, on that comment line?)
Discussions like this have come up from time-to-time. Currently there is no support for it.
Miguel
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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