[Chimera-users] trajectory rmsd

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 3 08:38:04 PDT 2012

Hi George,
If you want the best-fit RMSD (as if the atoms were superimposed) you would use the command "match", or if you want the RMSD in the current positions without fitting, you would use the command "rmsd".  Both of those commands allow specifying the exact atoms you want in the calculation.  Also, if you want the best-fit RMSD value but do not want to move the atoms, "match" has a "move false" option.  Example:

match #0:20-120 at n,ca,c,o #1:30-130 at n,ca,c,o move false


The command(s) could be used in a per-frame script in MD Movie.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 3, 2012, at 5:49 AM, George Tzotzos wrote:

> I'm writing to find out if it is possible to determine the rmsd of specific residues, say 20-120 (backbone atoms only) from a trajectory against the corresponding residues of an X-ray structures.
> I used the Movie tool to load the trajectory having loaded prior to it the reference structure. I couldn't find a way to compute what I described above.
> Your help as always is much appreciated
> Best regards
> George

More information about the Chimera-users mailing list