[Chimera-users] Possible bug in Chimera RMSD calculation

Elaine Meng meng at cgl.ucsf.edu
Sat Apr 3 09:55:12 PDT 2010

Hi Yasser,
It's not a bug.  The RMSD between 2 atoms equals the distance.  RMSD =  
root mean square distance, and if there is only one distance, the mean  
square distance is the same as the square distance, and then the root  
of that equals the distance.

The rmsd command calculates RMSD without fitting.  If you are trying  
to superimpose the atoms and then get an RMSD, you need to use the  
match command.  Of course, the superposition will not be unique with  
only 2 atoms.

Use the command "help rmsd" or "help match" to see the command manual  
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 3, 2010, at 8:13 AM, Yasser Almeida Hernández wrote:

> Hi all....
> In Chimera , i selected a single pair of atoms for RMSD calculation  
> with the command rms (rms #1:221.A at NE #0:221.A at NE) and it return the  
> distance between the atoms ????
> It would be a bug???
> Please check this....

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