[Chimera-users] Per-atom RMSD

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 8 14:05:16 PDT 2010

Hi Ibrahim,
Maybe I am not understanding your question correctly, but if you have two structures, the RMSD at each position is simply the CA-CA distance.  If you have three or more, it is more truly an RMSD.  But either way, yes, you can get that information after showing the sequence alignment of the superimposed structures.    

First superimpose the structures using whatever method you prefer, even some other program.  Here is a discussion of methods in Chimera:

Then use the Match->Align tool to generate a corresponding sequence alignment of 2 or more structures.

Then in the sequence alignment window, the "header" named RMSD can be displayed, if it is not already, by choosing Headers... RMSD from that window's menu.  The values are shown in a histogram over the sequences, but you can save them to a file as well, by choosing Headers... Save.

More about sequence alignment headers including RMSD:

These things are done interactively; currently there are no Chimera commands to do them. 
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 Oct 8, 2010, at 1:52 PM, Ibrahim Moustafa wrote:

> Dear Chimera,
>  I have a question regarding RMSD: I have two structures to superimpose
> using certain residues; and I am interested to get the RMSD value for each
> CA-atom in the structure. I wonder if there is a way to do that in Chimera?
>  I think there is no direct way; but I wonder if there is a script that can be used for that.
> For the developer: It might be useful to have a tool that can directly do that in Chimera
>      Many thanks for help,
>      Ibrahim
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