Hi Kevin,

Another trick to animate bonds appearing and disappearing is to use the movie crossfade command. This allows you to fade between any two scenes. So you start with a bond showing, then use

movie crossfade frames 25

and the following command undisplays the bond. This will cause the movie to fade between the bond shown and bond hidden state over 25 frames. In general it fades between the scene as it appeared just before the command to the scene just after the next command is executed. The fade does not appear on-screen -- only in the recorded movie.

Tom

On Feb 21, 2012, at 11:25 AM, Elaine Meng wrote:

setattr p color 1,0,0,.5
setattr p display 0

... where you could put the atomspec of the two endpoint atoms at the end of each command to control only that pseudobond, instead of all pseudobonds.

If you don't like the way the change in transparency looks, another alternative is to have the breaking bond become gradually thinner (attribute "radius") while the forming bond becomes thicker.

It's just as awkward to script because you would need a setattr command each frame the motion is happening (luckily it's easy to have motions go on as other commands are executed, just don't use a "wait" command after the motion command).

--Eric

  Eric Pettersen

  UCSF Computer Graphics Lab

                     http://www.cgl.ucsf.edu
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