[Chimera-users] matchmaker command

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 10 16:13:11 PDT 2006

Hi Matthew,
The superposition is a least-squares fit of the alpha-carbons of the  
residue pairs aligned in the sequence alignment:

I think it is reasonable to report the RMSDs in a paper if you give  
some indication of the number of alpha-carbon pairs that were matched  
(i.e. a low RMSD is less remarkable if the number of pairs matched is  
also low).  In general, you'd only want to compare among RMSDs if  
they were obtained with a consistent methodology (different sets of  
structures) or were for the same structures (comparing  
methodologies). It depends what you want to convey in your paper.

If you have the "Iterate" option turned on, the final RMSD and number  
of pairs used may both be quite low.  These values are not a good  
measure of overall structural similarity, because they also depend on  
the accuracy of the starting sequence alignment: if a large  
proportion of pairs are pruned during iteration, it could either be  
because the structures are dissimilar or because those parts of the  
alignment were misaligned.

I hope this helps,

On Jul 10, 2006, at 3:26 PM, Haas, Ryan Matthew wrote:

> Dear Chimera Users,
>   How does the matchmaker command perform its superposition?  Is it  
> a C-alpha superposition, or just backbone atoms, or all atoms?  Is  
> it appropriate to use these RMSD values obtained from “mmaker” in a  
> manuscript?
> Help is greatly appreciated.
>  Matthew Haas
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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