[Chimera-users] Tetramer using Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 24 15:55:27 PDT 2018

Dear Bárbara,
You can place four copies of your structure in any positions, but Chimera will not predict how the tetramer will form (which sides of the protein will form the interfaces).  You would have to determine that yourself, and then either place the copies by hand, using activation and deactivation to control which copies can be moved with the mouse

...or specify in the “sym” command exactly how to create and place the copies.  This can be difficult, because even if you know the symmetry group (say C4 or D2), you would also have to give the symmetry center and axis coordinates..

(If you had a structure of the tetramer of a homologous protein, then in Chimera you could match four monomers of your protein onto the four monomers in that tetramer.)

There are probably other programs to predict homomultimer structure from monomer structure, but I don’t have any experience with that myself.  They might look for multimeric homologous structures, collect homologous sequences and look at sequence conservation and covariation pairs, and/or use protein-protein docking.

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

> On Aug 24, 2018, at 2:29 PM, Bárbara Abrahim Vieira <babi_abrahim at hotmail.com> wrote:
> Dear all,
> We wish apply in our research the Chimera system. 
> Initially, we build our model (monomer) using ab initio and then, we will investigate the active site using docking. However, it is known that the protein is a tetramer.
> Then, we need to create a tetramer, without any pdb homologous, is it possible?
> Thanks for your time,

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