[Chimera-users] Measurement similarity protein structure

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 9 11:22:50 PDT 2019

Hi Nail,
There is no reason the 3D superposition and RMSD result has to be different. The two scoring methods for sequence alignment might give the same sequence alignment, or even if the sequence alignment is partially different, the iterative 3D fitting starting from the sequence alignment might end up using the same positions of the proteins in the final fit.

If you use the option to show sequence alignment, it will show the sequence alignment and draw light orange boxes on the alignment indicating the positions of the 3D structures used in the final fit.

For more explanation of how Matchmaker works, see the manual page.  There is also a publication, if you really want to read even more.

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

> On Jul 9, 2019, at 2:21 AM, Nail Besli <beslinail at gmail.com> wrote:
> Hi 
> I superimposed two proteins in chimera with winch algorithms( blossom62) and p250. The result is the same. Why is the result same for both two proteins, although I tried two different algorithm settings? I  am using the chimera's MatchMaker tool. The only thing different is the sequence alignment score. I attached the result file.
> kind regards

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