[Chimera-users] RMSD supports symmetry?

[Elaine Meng]

Hi Kevin,
The "rmsd" and "match" commands do not figure out which atoms are  
chemically equivalent or symmetrically arranged and try all of the  
possibilities.  If the atoms are not specified by name in the command,  
they will be sorted by name and the sorted lists used for pairing.   
You can explicitly give the atom names in the command in whatever  
order you like, however.  For a ring that could be flipped, for  
example, you could issue two "rmsd" commands and then take the lower  
of the resulting RMSD values.  The commands including all the atom  
names could be rather ugly and long, but you could possibly minimize  
the pain with aliases if the names are stereotyped (say within  
standard PDB residues PHE and TYR).

More details on how these commands work:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Sep 11, 2009, at 4:04 PM, Kevin Wu wrote:

> Hi all,
> I'm wondering if the RMSD function in Chimera will correctly  
> calculate RMSD when two molecules are compared. For example, if a  
> benzene ring is flipped, will the RMSD stay the same? Furthermore,  
> how does Chimera do this comparison?
> Thanks!
> Kevin