[Chimera-users] Alignment of repeated domains

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 26 14:49:38 PST 2018


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:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#initial>

… or if using the “matchmaker” command, you could specify residue number range directly in that command to restrict the fit, as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>

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
-----
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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