[Chimera-users] Building protein-protein complex with known interacting residues

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 3 14:55:39 PST 2014

Hi Fei,
Chimera does not do anything to the relative positions of the structures in the files that you open. Although you can rotate and move the entire view, the relative positions of the structures are simply based on the input coordinates (X,Y,Z read from the file).

In Chimera, you could change the relative positions manually by moving the proteins separately from one another,

(A) interactively with the mouse:  you can freeze some structures by unchecking the boxes under the command line (or equivalently, the "A"ctive boxes in the Model Panel) so that only the other models respond to the mouse


(B) with translation and rotation commands: "move" and "turn" allow moving only certain models if you use the "models" keyword

You would probably color the interacting residues differently to help guide these movements. However, I agree completely with Aldo that the result would only be approximate.  One reason is that is difficult to manually position the structures to fulfill multiple constraints and/or restraints.

You may want to look for other software to perform protein-protein docking (like ClusPro as Aldo said, or others) and/or simulations to satisfy multiple restraints.  Chimera does not have these capabilities, but it could be used to view the results.  In the future we would like to have an interface to Sali group software (based on the Integrative Modeling Platform) for these types of calculations.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 2, 2014, at 12:08 PM, fei.wu at chem.utah.edu wrote:

> Dear Chimera Team,
> I am studying the interactions between three enzymes with their biological
> assembly structures available in PDB. Using mass spectrometry, I have been
> able to identify interfacial residues, and what I want to do is build up a
> super complex (made of the three proteins) in a desired way that these
> proteins are oriented by interactions between experimentally-determined
> residues. Would you please tell me that, if I can make or draw this in
> chimera? And I am also trying to compare experimentally-proposed complex
> structure with simulated structure. Is there a specific way in chimera to
> simulate interactions between two or more proteins? I found that when I
> opened multiple protein files in one session, chimera would gave me a
> complex of these proteins (not always true with different pdb files). Is
> this an automatic generation of simulated protein complexes or just a
> superimposition of part of proteins?
> Thanks,
> Fei

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