[Chimera-users] Generate the tranfromation or bio matrix from the docking complex using Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 14 10:32:10 PDT 2017

> On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai at fiu.edu> wrote:
> Dear Meng,
> I have a cylindrical symmetry protein complex modeled with the protein-protein docking.  Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the  matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera?
> Thank you, and I look forward to hearing from you. 
> Kind regards,
> Elumalai

Dear Elumalai,

I’m CC-ing chimera-users at cgl.ucsf.edu … it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions.

I’m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing.  If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices.

However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex.  So if I understood your problem correctly, you would need to find some other program to do this.  I haven’t done it myself, so I don’t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices.

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

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