Peter,
Ah, OK, I understand. yes, right. Potential energy maps. Are you
specifically interested in loading a set of models and then accessing them
via this 1:1 correlation of grid points to models? Where I've seen this work
reasonably well is in the (now defunct) CAChe/Sygress modeling package. I
did like the way they did that -- two windows side by side -- click on the
graph to display the structure.
Thus, what we are doing here is
a) establishing an X,Y correlation between the graph and a model set:
frame @{someFunc(x,y)}
b) graphing some parameter as a function of the same x and y:
isosurface functionXY ....
c) coordinating two displays (two applets, perhaps?)
set pickCallback
Sort of a 3D equivalent of
http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm
So the answer is, yes, Jmol can do this. But it would take some work to
build the page that would do it smoothly. I don't know that there would be
any built-in option to consider, just because I don't think there is a known
data format that includes all that in one easily loadable package, and
plotting XYZ maps in a general sort of way is not easy.
This is the sort of thing that people build special applications for,
embedding Jmol in the application as the way to display the structures, but
using other resources for the other displays.
Certainly a nice project for someone....
Bob
On Fri, Apr 2, 2010 at 8:36 AM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
> On Fri, Apr 2, 2010 at 1:04 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> what does the data look like?
>>
> Here's a typical example:
> http://chem.wayne.edu/~hbs/chm6440/PES.html<http://chem.wayne.edu/%7Ehbs/chm6440/PES.html>
>
> In this there is an implied function E(x,y) where x and y are two
> geometrical coordinates. They are not normally simple bond lengths and
> angles but combinations of them. Examples are "symmetry coordinates" which
> often map onto vibrations and "reaction coordinate(s)" the variation of
> geometry during the reaction. There are normally many dimensions (e.g. 3N-6
> for non-linear molecule) but the diagrams are normally restricted to 1,2, or
> 3 geometrical coordinates so they can be pictorially displayed.
>
> Each point (x,y,z,p,q...) corresponds to a configuration of atoms which
> could be displayed in Jmol. So moving the mouse over the surface would show
> the variation of the structure coupled to the variation in energy.
>
> A typical example of a 2D PES is the variation of energy with 2 torsion
> angles such as in the "alanine dipeptide" (actually acetyl alanyl
> methylamide). This is a classic introduction to molecular mechanics. Here's
> a small bad picture:
> http://ats.vimeo.com/241/156/24115602_200.jpg
> the two axes are the two main torsion angles phi and psi
>
>
>
>>
>>
> --
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
>
>
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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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