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

[Tarazkar, Maryam]

Hi Elaine,
So I have a protein that is monomer (Ebour). I want to make it as a dimer based on the template of 6eni. (in fact 6eni is the closet hit to Ebour based on what Modeler predicts). Note that 6eni is dimer.
Given the information above can you expalin me or refer me to a reference how I can make a dimer of Ebour using Chimera?
Thank you,
Maryam

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, September 14, 2020 12:19 PM
To: Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: Is it possible to make a dimer from a monomer protein in chimera?


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




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