[Chimera-users] Structure superimposition - RMSD

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 16 09:57:04 PST 2011

Hi Suda,
Matchmaker does pairwise superpositions to the reference, so even if you chose to match structures B,C,D to A, it will perform pairwise matches and report pairwise RMSD for A-B, A-C, and A-D.  All of those should be in the Reply Log, but there is various other stuff between them such as parameters listings, so you would need to scroll up to see them.

However, to get an overall RMSD of more than two structures, after you run MatchMaker you would run Match->Align to make a multiple sequence alignment (instead of the pairwise ones created by MatchMaker).  Match->Align is in the menu under Tools... Structure Comparison.

Besides overall RMSD it will also give you other measures of structural similarity (SDM, Q-score), and in the output sequence alignment there will be an RMSD histogram above sequences showing the per-column values.

HOWEVER, be aware it will take a pretty long time to run Match->Align on 10 structures, especially with iteration.  I would try it without iteration first (which still might take a pretty long time, many minutes) and see if the resulting sequence alignment looks good enough.

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 Nov 15, 2011, at 8:31 PM, Suda Parimala Ravindran wrote:

> Hi all,
> I have a set of protein structures (about 10) that I need to superimpose. I have used Matchmaker and superimposed by choosing a reference structure. I want to know how to calculate the overall RMSD of the superimposed structures? Where do I lokk out for it? I have checked the Reply log window, but it gets displayed only for some, whereas for others it does not. Please help..
> Thanks,
> -Suda

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