> 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.
This is exactly what we do in our SVG and all elements appear in all frames. It could be useful to have an attribute visibility="hidden" for turning off the display of certain atoms
Q: Would this type of restriction conflict with any of these applications?
No.
(The only thing I can think of is nuclear reactions ... where the atom type would change :-)
This might be modelled in some simulations (e.g. what is the theoretical effect of mutating an aluminium to silcon, but they aren't top priority
> 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.
Understood
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.
OK - I will help where possible.
The general theme might be (say)
A + B-C ==> A-B + C
atom A reacts with molecule B-C creating a bond A-B and destroying B-C. We might wish to display the A-B bond initially as null, then as a dotted line then as a full bond, possibly increasing in opacity or size. Vice versa for B-C
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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