[Chimera-users] Possible bug in Chimera RMSD calculation
meng at cgl.ucsf.edu
Sat Apr 3 09:55:12 PDT 2010
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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