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

[Elaine Meng]

Hi Katryna,
I think what you want is available, but only via keyboard shortcuts.   
You have to first enable shortcuts as described here:
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html 
 >

The you can use the "comparing domain orientation" shortcuts "ab" and  
"ai" described briefly here:
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/alist.html#molalign 
 >

and in a more detailed example here:
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/alist.html#abdetails 
 >

A limitation is that the residue numbers and chain IDs need to be the  
same between the different orientations being compared.   The output  
is two rectangular slabs and in the Reply Log, RMSD, number of atom  
pairs, and angle of rotation.  I don't see anything about translation,  
however.

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Sep 11, 2008, at 9:39 AM, KATRYNA CISEK wrote:

> Dear Chimera developer,
> I would like to analyze a set of dimer structures based on a  
> reference dimer structure.
> Unfortunately a simple RMSD calculation does not capture the  
> translational/rotational
> shift that occurs. Is it possible to extract a plane of rotation and  
> degree of rotation between
> two structures in chimera?
> Thanks,
> Katryna