> 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.
Be advised that I have a unique perspective ... since I have never actually created an animation :-) > 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? It is currently not implemented, but I plan to put in a restriction that an 'animation' needs to contain the same number and the same elements in the same order in every model. Q: Would this type of restriction conflict with any of these applications? (The only thing I can think of is nuclear reactions ... where the atom type would change :-) > 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. The animation in Jmol is based upon distinct 'models'. So one can basically animate any type of file. Today one can see animated multi-frame .xyz files and animated animations in multi-model nmr pdb format. Go to: http://www.jmol.org/demo/animation > 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. I didn't understand a lot of this. Let me try to digest it. Miguel ------------------------------------------------------- This SF.Net email is sponsored by the new InstallShield X. >From Windows to Linux, servers to mobile, InstallShield X is the one installation-authoring solution that does it all. Learn more and evaluate today! http://www.installshield.com/Dev2Dev/0504 _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
