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: <http://salilab.org/modeller/discussion_forum.html> Good luck, Elaine ----- 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