[Chimera-users] RMSD supports symmetry?

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 11 17:21:23 PDT 2009

I forgot to mention that I recommend using the Chimera snapshot from  
Aug 20, or even a newer daily build, because now commas in command- 
line atom specifications imply ordering -- in version 1.3, comma- 
separated models, residues, or atoms are not necessarily used in the  
order typed.  To specify atoms in a particular order in those older  
versions it is necessary to enter something like @ca at cb@cd1 at ce1  
whereas in the newer versions, @ca,cb,cd1,ce1 also specifies order.

On Sep 11, 2009, at 4:59 PM, Elaine Meng wrote:

> 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
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