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, opacitymolecule:
colour, visibility, position, rotation, opacity, velocity, surfaceatom
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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