[Chimera-users] Protein RMSD

[Elaine Meng]

Hi John and everybody,
I forgot to mention the following additional ways to calculate RMSD  
in Chimera if you are working with a conformational ensemble  
(different conformations/configurations of the same set of atoms):

- if the ensemble is opened as a trajectory in MD Movie, you can  
calculate an all-by-all RMSD map
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ 
framemovie.html
(go to the "RMSD Analysis" section)
... also covered in a tutorial
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
ensembles2.html#part2

- if the ensemble is present as multiple MODELs within a single PDB  
file opened the normal way in Chimera, you could use the  
EnsembleMatch tool
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
ensemblematch/ensemblematch.html
... also covered in a tutorial
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
ensembletut.html

I don't know if these pertain to the original question, but I mention  
them for completeness.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html