[Chimera-users] aligning proteins based on sequence alignment

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 23 08:14:13 PDT 2020

Dear Neha,
You would just start Chimera, and then

(1) open the sequence alignment, assuming it is one of the formats Chimera knows:

Then a sequence window (Multalign Viewer tool) will automatically appear, showing the alignment.

(2) open the protein structures

The structures will probably associate automatically with the sequences in the alignment if they are similar enough.  You can tell by seeing a colored box on the name of the sequence in the alignment window and/or by clicking into the sequence window and putting the cursor over the sequence to show status information that it is associated. If they are not associated automatically then you can do it manually with sequence window menu: Structure... Associations.  Sequence-structure association and how to do it manually is described here:

(3) use sequence window menu: Structure... Match, choose the options you want in the resulting dialog.  Options are described here:

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

P.S. your description of Matchmaker is not quite right.  Actually it first makes a pairwise sequence alignment, then uses it to superimpose the structures.  To make a sequence alignment based on two or more already superimposed structures, you would instead use the Match->Align tool.

> On Apr 23, 2020, at 12:44 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> Dear List,
> I know Chimera can provide sequence alignments based on structure superimposition (matchmaker).
> I want to superimpose proteins based on the sequence alignment.Is there a way to do this?
> Thanks,
> Neha

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