[Chimera-users] match-align using just selected protein areas ?

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 12 09:35:39 PDT 2014

Hi Marek,
Yes, if you mean MatchMaker (Match->Align does not align the structures, it just makes a sequence alignment from a structural alignment you already made).

In the MatchMaker GUI, there is a "Further restrict matching to current selection" setting:

In the matchmaker (mmaker) command,
... it is similar but you instead specify the residues directly instead of selecting 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 Mar 11, 2014, at 6:53 PM, Marek Maly wrote:

> Hello,
> I would like to know if it is possible in Chimera
> align two proteins let say protein A and protein B,
> but just using selected subsequences A_sel, B_sel
> (i.e. just the selected subsequences are going to be
> optimally matched and the rest of both proteins is not involved
> in the matching process/calculation) ?
>   Thank you in advance !
>       Best wishes,
>          Marek

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