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On Wednesday 02 June 2004 14:50, timothy driscoll wrote: > Miguel sent (2004.06.02 at 11.01a [+0200gmt]) : > >>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 :-) > > unless I misunderstand your suggestion, I would argue against such a > restriction. it is often helpful to animate the transition from bound > to unbound states of an enzyme, for example, where the bound state > structure contains ligand but the unbound state does not.
I see two options here:
1. make the ligand unvisible in the last half of the animation (or so...) 2. move the ligand away from the enzyme to get to clearly separated species
(or a combination of both)
Much easier than explicitely marking which atoms correspond in each frame...
I completely agree. We have found that taking this approach in 2D makes a dramatic change to the usefulness of the representation. All atoms present in all frames in the same order. In some cases atoms can be hidden or moved out of frame. We also create a complete list of all bonds and then make them invisible where they don't occur. Works very well.
Egon
- -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6
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