[Chimera-users] Dimer construction from a monomer generated using Modeller

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 19 10:58:38 PDT 2010

Dear Akshita,
I don't think this is something you can handle effectively with  
Chimera.  Instead, it might be possible to:

(a) from the trimer of the model you have now, re-model just the loops  
using Modeller so they don't conflict with each other
- OR -
(b) instead of modeling a monomer from the template monomer, use  
Modeller to model a trimer starting from a template trimer, which  
might also the loops more sensibly

However, I don't know either of these things can be done, or how to do  
them, since I don't have direct experience.  You might try asking on  
the Modeller forum:

Good luck,
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 19, 2010, at 3:33 AM, akshita kumar wrote:

> Dear Members,
> Using 1T3D as template, we have generated a homology model via  
> Modeller. As the biological unit is a trimeric structure we need to  
> generate trimer of the model too. Therefore we undertook structural  
> alignment of the model and individual template 1T3D chains ("a, b ,  
> c"). However in our model the loop region that falls at the  
> interface between two dimers is much  longer and as a result the  
> loops between dimer overlap each other.
> Can anybody please suggest a solution for generating a dimer/trimer  
> from the monomer built using homology modelling.
> Thanks
> Akshita

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