-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 02 June 2004 10:43, 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 CML syntax currently used in Jmol is: <list dictRef="jmol:animation"> <molecule id="FRAME1"/> <molecule id="FRAME2"/> <!-- etc --> </list> I guess the molecule element could use a @dictRef="jmol:animationFrame" See for example CVS samples/cml/SN1_reaction.cml > The primary uses > are conformational transitions, molecular dynamics and chemical reactions. > Are there others? Not that I can think of at this moment... well, maybe demo's ... i.e. custom movies... those are hand-made, e.g. to visualize a biochemical process... but which are not the result of a program... > 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. I think Miguel can best respond to these... I think most is implemented except for opacity, surface and 'curly arrows'... Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAvZb0d9R8I9Yza6YRAvnqAJ4hH0OKOXYxQ2kVabG7QE12IbV+6gCgoAk8 EyO7VwXSU0bZJ0601jWqzTA= =bK9j -----END PGP SIGNATURE----- ------------------------------------------------------- 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
