[Chimera-users] rotational/translational shift from reference structure

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 15 13:03:21 PDT 2008

On Sep 15, 2008, at 3:13 AM, julien(GWDG) wrote:
> I wanted to know if there is a way in chimera to get the same  
> information as the shortcut ai but for small molecule.
> When I use "ai" with small molecule I get the message : "not enough  
> back bone atoms", which is normal because there is no back bone atom  
> and because the molecule is small.
> But I have a rigid docking of one ligand and I would like to see  
> what is the rotation components (rotation matrix) between the  
> different pose. Of course one could just do it by a small C++ script  
> but if chimera has it already implemented it would be easier for us.
> Thank you for your support and your nice soft.
> many greetings
> Julien

Hi Julien,
Thanks for the compliments!

There are commands to do a similar thing, although not in one step.   
The "match" command will fit the specified atoms and give an RMSD.   
Unlike the ai shortcut, it moves one structure onto the other.

Then you can use the "matrixget" command to report the transformations  
of the structures.  However, note this reports the total  
transformation: all movements that have been applied, not just what  
happened in the fitting step.  To get only the fitting transformation,  
you would first need to "reset" the reference structure so it is  
untransformed, then "match" the other structure onto it, then use  

For example, using two different structures with FAD:

open 1f3p
open 2npx
preset apply int 1
match #1:fad #0:fad
matrixget -

Don't move anything around by hand between "reset" and "matrixget"!   
The last command sends the matrix info to the Reply Log.  In this case  
the atoms in FAD are ordered and named consistently, so I could simply  
use the residue name in the match command.  If you only wanted to use  
certain atoms, or if the atoms were not ordered and named  
consistently, you would have to give the atom names in the match  

I hope this helps,

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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