[chimera-dev] Building a dimeric protein model

[Elaine Meng]

On Oct 15, 2020, at 1:41 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> Hi
> I've built a monomeric model using Chimera's MODELLER interface. I was wondering whether it's possible to use this model in Chimera to create a dimer. The dimer of the protein that I'm studying is composed of two antiparallel symmetric monomers.
> Thank you
> Tiglath
> 
Hi Tiglath,
Sure, but you would need to know the proper positioning of the two monomers in the dimer.  There is nothing in Chimera to figure that out automatically.  If there is a known dimer structure of a related protein and you think your modeled protein forms a similar dimer, you can simply 

(1) save your new monomer model as a PDB file
(2) start a new Chimera, open that new PDB file two times so that you have two copies open
(3) open the known dimer structure of the related protein, let's say it has chains A and B
(4) superimpose one copy of your monomer model onto chain A of the known dimer structure, and superimpose the other copy of your monomer model onto chain B of the known dimer structure.  Different methods of superimposing structures are discussed in the link below.  Probably the easiest is to use the Matchmaker tool.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

(4) close the known dimer structure, and what you have left is the approximate dimer with two copies of your model, which can be saved as a session, or combined into a single model (see "combine" command) and then saved as a PDB file.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

Alternatively if you have a dimeric template structure you can use Modeller to make a dimeric comparative model directly, but to do that you would have to use the Modeller interface in our newer program ChimeraX.  The one in Chimera only allows modeling monomers. Modeller interface in ChimeraX:
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>

This chimera-dev e-mail address is mostly for programming questions.  For general user questions like this (for future reference) a better address to use is chimera-users at cgl.ucsf.edu CC'd here, and there is also a similar address for ChimeraX: chimerax-users at cgl.ucsf.edu

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