[Chimera-users] Modeller awareness of other proteins

Elaine Meng meng at cgl.ucsf.edu
Thu May 26 09:12:33 PDT 2016

Hi Juan,
Sorry no, not with the Chimera Modeller interface.  Modeling a multimer or complex (taking into account other chains) requires running Modeller outside of Chimera, a harder task if you don’t have experience doing that already.


I don’t know if your initial model was from comparative modeling or just filling in missing segments without a template. Either way, you could try generating multiple conformations and seeing if any of them are better at avoiding the other proteins.  If the initial model is from comparative modeling, you could subsequently use the loop remodeling interface and just get ensembles of new conformations for the problematic segments, in the same way as modeling missing segments.  I.e., increase “number of output models” to give yourself a larger sample of conformations and see if any of them make more sense relative to the whole complex.  It will still ignore the other chains, but you will have more possibilities to choose from.

Other than that, you could always try rotating bonds yourself, but that’s generally a combinatorial problem not well solved by interactive human tweaking. (There is minimization too, but it generally has very limited ability to fix structure problems with a rugged energy landscape.)

I hope this clarifies,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 26, 2016, at 8:55 AM, Eiros Zamora, Juan <j.eiros-zamora14 at imperial.ac.uk> wrote:
> Dear Chimera experts,
> I’ve got a system of three interacting proteins, and each of them is missing some linker regions in the crystal structure.
> I’ve succesfully used the Modeller interface in Chimera to add these regions, but the problem I’m facing now is that it adds the residues without considering that other atoms from another protein of the system are in the way.
> Is there a way to tell Modeller to be sensitive to other structures nearby?
> Thanks for any comments, 
> Juan Eiros Zamora / PhD Student 

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