[Chimera-users] Is it possible to make a dimer from a monomer protein in chimera?

[Elaine Meng]

On Sep 14, 2020, at 12:07 PM, Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu> wrote:
> 
> Hi Elaine,
> I am wondering can you refer me to a tutorial in Chimera where it explains how to make a dimer protein from a monomer?
> Thank you,
> Maryam

Hi Maryam,
Yes, of course you can do it, but there is no specific tutorial:  how to do it really depends what information is in the input file, what you know about the structure, etc.  If it is an entry in the PDB database you could just try fetching the biounit directly and seeing if it  is a dimer.  E.g. menu File... Fetch by ID, use the "PDB (biounit)" choice.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/fetch.html>

Some files have symmetry information in their files so that you can build the multimer with the "sym" command, e.g.

open 1fav
sym #0 #0

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

If it is not yet a deposited structure, but you already have a related structure that is a dimer, you can just open two copies of your protein and match it onto the two monomers of that other structure, e.g. with the Matchmaker tool.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

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