[Chimera-users] Moving PDB between 3 orientations

Thomas Goddard goddard at cgl.ucsf.edu
Mon Nov 23 14:32:24 PST 2009

Hi Chris,

   To show a molecular model moving between three orientations you would 
use Chimera commands savepos and reset and matrixcopy.  Here's how I'd 
go about it.

  First put copies of the molecular model at all 3 positions.  If you 
have saved these in 3 Chimera session files I would open all 3 sessions 
telling Chimera not to close the previous session when I open each new 

   Now open a 4th copy of the molecule.  Suppose the original 3 copies 
are model numbers #0, #1, #2 and the 4th copy is model #5.  To align the 
4th copy with #0 use

	matrixcopy #0 #5

(The matrix being copied is the positioning matrix, the rotation and 
shift that places the molecule in the scene.)

   Record the positions of all the models now with

	savepos p0

The name p0 could be anything.  We'll use it later with the reset 
command.  Also save positions with the 4th model in the other 2 states:

	matrixcopy #1 #5
	savepos p1
	matrixcopy #2 #5
	savepos p2

Now to move the 4th model pack to position 0:

	reset p0

and to move it from position 0 to 1 over 50 frames

	reset p1 50

and then from 1 to 2

	reset p2 50

In a movie recording command script remember to put a "wait 50" between 
these two commands so they don't both try to run simultaneously.


There is a movie making tutorial that explains some of this:



-------- Original Message --------
Subject: Re: [Chimera-users] how to link three EM confirmations in morph map
From: Chris Arthur
To: Thomas Goddard
Date: 11/23/09 1:40 PM

> Hi Tom,
>     I have one other question. I have a pdb (the same pdb loaded into 
> chimera 3 times), that I have docked into three distinct EM maps. I 
> would like to make a movie showing the rotation of the pdb as it goes 
> from one docked state to the next, to the next. I guess this would be 
> similar to the morph command but for pdb's instead of EM maps. Any 
> suggestions?
> Thanks,
> Chris
> The Scripps Research Institute

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