[Chimera-users] calculating NxN RMSDs

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 25 15:07:09 PDT 2013

Hello Hira,
If the structures have exactly the same atoms and bonds (same names, same order) then you can open as trajectory and use the RMSD analysis in MD Movie, which will automatically calculate all N x N values and allow you to save the RMSD values to a file.  See the MD Movie manual, especially the parts about input and RMSD analysis:

If instead they are different proteins and you are using MatchMaker, then you would need to write a script to process the N x N pairs or comparisons, then take the output values from the Reply Log.  There is  a "matchmaker" command that has the same features as the MatchMaker GUI. 

See also information about scripting to process multiple PDB files:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 23, 2013, at 1:18 AM, Hira Saleem wrote:

> Respected fellows!
> i need  help from you. actually i am working on my project and uses chimera for this . i have a problem because i have a huge data and i have to collect RMSD value of 10000 pdb ids in a 262 by 262 matrix. just wanted to know if there is another procedure to collect value instead of collecting manually. because it takes too much time and very hectic work.
> waiting for your precious suggestion and will be very thankful to you.

More information about the Chimera-users mailing list