[Chimera-users] animation

Tom Goddard goddard at sonic.net
Wed Apr 20 10:49:52 PDT 2011

Hi JP,

   Here are some ideas about how to do these animation steps.

1) To rotate 3 volumes each about its own center you can use the 
"independent" center of rotation method, command "cofr independent".  
That won't allow you to easily initiate rotation of each model at a 
different time.  To do that it is simpler to just use the "turn" command 
to start each model rotating.  For example,

turn y 3 120 center #0 model #0
wait 60
turn y 3 120 center #1 model #1

will rotate model #0 about its own center in 3 degree steps for 120 
steps (360 degrees total) about the vertical screen axis.  60 steps 
after that has started (wait 60) model #1 will start rotating in the 
same way.

2) To make one residue after another appear you would use

     display :82.A
     display :83.A
     display :84.A

You could put "wait 5" between each to separate the appearing residues 
by 5 frames, otherwise you'd get one appearing each frame.  It's a pain 
to have 100 commands to show 100 residues and you may want to got to 
instead use Python script to do this.

     from chimera import runCommand
     for i in range(82,155):
        runCommand('display :%d' % i)

Fading in with transparency also requires lots of commands, one command 
to set each transparency level.  For surfaces there is a single command 
(surftransparency) that can do this, but no command to fade in molecules 
that way.  Again Python would be the way to go.

3) To smoothly vary colors, you could use the multiple command approach 
described in 2) or you can use the "movie crossfade" command 
demonstrated in the following video:


It allows you to smoothly interpolate between any two scenes.  That 
works well for color changes.  But it won't work well if you want color 
to change while at the same time objects are moving.  In that case you'd 
have to use the multiple color commands approach.


> hello,
> i would like to ask a question about animation. i would like to achieve
> the following:
> 1. i have 3 different volumes, so when i put them next to each other, i
> would like to have each of them to rotate around it's own axis. an
> additional feature would be to start the rotation of each of the volume
> at a different point of time.
> 2. i would like to make certain parts of pdb appear slowly, either
> through change of colors from transparency or nucleotide/aminoacid at a
> time.
> 3. i would like the colors of a specific volume/pdb to "pulsate",
> meaning to start up with color nr 1, through 2 or 3 different colors to
> color nr 2.
> at the present moment i don't really know how to do those, would you
> have any hints ?
> thank you
> best regards,
> JP Armache
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> Chimera-users at cgl.ucsf.edu
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