[Chimera-users] Animate a Reacton Mechanism?

Tom Goddard goddard at sonic.net
Tue Feb 21 15:59:58 PST 2012

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.


> 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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> Chimera-users at cgl.ucsf.edu
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