[Chimera-users] [chimera-dev] Problem with Matchmaker tool

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 20 17:57:41 PST 2020

Hi Tiglath,

(1) 1av1 is not a dimer.  It is a tetramer, 4 copies of the same peptide, chains A,B,C,D.  See:

(2) Matchmaker is working correctly, but you have to choose "Specific chain of reference structure" (not "Best-aligning") and then specify exactly which chain of 1av1 you want as the Reference.  You have to use it twice, so that you can match #0 to one reference chain and #1 to a DIFFERENT reference chain.  Otherwise they will both go to exactly the same place because they will match the same chain, which I guess is what happened to you before.

Actually, maybe you need to use it four times with four copies of your model if you expect to get something that looks similar to 1av1.

The chimera-users at cgl.ucsf.edu address is recommended for "how to use" questions, so I'm CC-ing it here.  The chimera-dev list is more for programming questions.

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

> On Nov 20, 2020, at 5:17 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> Hi
> For some reason I'm not able to use the matchmaker tool to build a dimer model of the protein I'm studying. Here are the steps that I use:
> 	• I open twice the monomer model
> 	• Then I open the dimer template, then click on the Matchmaker tool.
> <image.png>
> 3. In the Reference structure panel I click on the dimer template (1AV1)
> 4. In the Structure(s) to match panel I click on monomer#0 (Human Monomeric Apo A-I, the protein I'm studying) then click OK
> 5. Then I click on monomer #1 followed by OK
> But when I close the dimer template I get back the monomer not the dimer model of the protein. I'm not sure what I'm doing right.
> Thanks
> Tiglath 

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