My two cents: Somewhere along the way someone is going to have to decide what is conserved and what is not. Chemically speaking, atoms are conserved but bonds are not. So Peter's animations will all have the same number of atoms throughout (I agree that something like ligand/enzyme would best be described with all atoms present.) But some will imagine a reaction sequence such as that Diels-Alder reaction, where bonds change. Now, with XYZ format, you sort of get that automatically, based on on atom-atom distances. "Bonds" are sort of nebulous, ambiguous things anyway, so I doubt that anyone would argue that a bond HAS to be made here or there. But there will be reaction sequences when one might want to emphasize a bond that is coming in and is longer than the given bond. I guess what I'm arguing for is a flexibility in bonding but not necessarily in number of atoms. Here's a question: what happens if, upon an animFrameCallback you send a script to the target model?
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?
2. Could such a script be incorporated somehow right into the CML or MOL description (say, for instance, on that comment line?)
Bob
Peter Murray-Rust wrote:
At 09:39 02/06/2004 +0200, Miguel wrote:
I would be very interested in being able to read animations in CML and I'd like the Jmol community's feedback before finalising the details of the format. I am using "animate" to describe the visualisation, in a defined order, of a number of snapshots of molecular structure. The primary uses are conformational transitions, molecular dynamics and chemical reactions. Are there others?
In principle one can animate the chemistry (molecular structure) and also the visualisation (display styles, visibility, opacity, etc.) Here are some suggestions and I'd be grateful for what Jmol can do at present and would like to do in the future. I am using molecule, atom and bond as the primary objects, though clearly with graphical objects (boxes, spheres, etc.) there are other possibilities. The display properties are informed by SVG which can animate most CSS attributes and several others. We have been animating reactions using 2D SVG graphics and currently use many off:
graphical object (and text): colour, visibility, position, rotation, opacity
molecule: colour, visibility, position, rotation, opacity, velocity, surface
atom colour/style, visibility, opacity x,y,z velocity elementType (not common, but possible in free energy perturbation)
bond
existence (important for reactions. We need to be able to insist on bond depiction, regardless of covalent radii)
display style (transition from solid to dotted, etc.), colour, radius, etc.
order (double may change to single, etc)
position. It may be useful for bonds to "swing" from one part of connected atoms to another (represents curly arrows in reactions)
The SVG animations give people a new and often exciting feel about chemical reactions. If Jmol can do this in 3D it will be incredible. I suspect that much of it is already there in some form.
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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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
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