[Chimera-users] Movies and Symetries

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 21 11:40:43 PST 2020

	As far as I know you will have to run a script every frame to create the assembly and color it the way you want.  It is pretty easy to run a script every frame of a trajectory.  Use MD Movie's Per-Frame→Define script... menu item to bring up a dialog to run commands every frame.  In the dialog make sure you change the "Interpret script as" value to "Chimera commands".  The command to expand the BIOMT records is:


This will create full atomic coordinate copies.  You could use the "surfaces true" argument to only make surface copies instead.  I'm a little hazy on exactly what you are saying about how you want to do the coloring, but whatever it is you just need to determine what the equivalent commands are and add them to the script.  Each symmetry copy has its own model number (look at the Model Panel), so to color them you should be able to do something like "color red #1.1".
	Clicking OK in the dialog will accept the commands you've entered and you should be able to just play through your trajectory normally.  The playback will likely be slow due to the overhead of running 'sym' every frame.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Dec 21, 2020, at 7:15 AM, Stéphane DUQUERROY <stephane.duquerroy at pasteur.fr> wrote:
> Hi,
> I generated a set of coordinates in a single PDB file for a movie (coord flanked by MODEL / ENDMDL tags)
> I can read it and play it with MD movie menu
> The PDB File has also BIOMT matrices set for displaying the biological assembly
> My question is how can I play the movie with multiscale model? 
> How Can use automatically the color zone tool to color various protomer instances for all intermediate conformations? 
> (The only way I know for doing that is to generate and select all sym instances but they moved with each of the models!)
> S Duquerroy
> -- 
> --------------------------------------------
> Duquerroy Stéphane, PhD,
> Assistant Professor, Univ Paris Saclay
> Structural Virology Unit, Institut Pasteur
> 28 rue du Dr Roux, 75015 Paris - France
> 33 - (0) 140 613 575
> --------------------------------------------
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