[Chimera-users] Alignment of repeated domains

Benitez De La Fuente, Francisco fran.benitez at botany.ubc.ca
Fri Jan 26 15:17:59 PST 2018

It perfectly solved my problem. 
Thanks so much Elaine for your help and quick answer.

Have a good Friday!
Francisco Benitez.
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Friday, January 26, 2018 14:49
To: Benitez De La Fuente, Francisco
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Alignment of repeated domains

Hello Francisco,
You can specify just the part to use for the alignment. In the graphical interface (MatchMaker dialog), you would select the part of the structure you want to use and then turn on the option to "Further restrict matching to current selection,” described here:

… or if using the “matchmaker” command, you could specify residue number range directly in that command to restrict the fit, as described here:

Example: mm #0:50-100.A  #1
… will only use residues 50-100 in chain A of the reference structure #0

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

> On Jan 26, 2018, at 12:15 PM, Benitez De La Fuente, Francisco <fran.benitez at botany.ubc.ca> wrote:
> Hello,
> I'm using the tool MatchMaker to align different structures.
> My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain).
> How can I do so I can exclude the part of the protein already aligned in new alignments?
> I hope I explained myself and thank you in advance.
> Francisco Benitez.

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