Hi Tiglath, (1) 1av1 is not a dimer. It is a tetramer, 4 copies of the same peptide, chains A,B,C,D. See: <https://www.rcsb.org/structure/1AV1> (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@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 ----- 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@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