Hi; Yes you can do it. I you are sure about the interaction sites and the orientation, I will suggest you to build manually the complex and use the resulting model as template and build a new model. But this time use the "strongest" optimization routine (see the manual it is routine 3 or 1 I don't remember". Also depend on the result you may have to eliminate some restraint that may bias the final model.

I hope it helps. Eric

------------------------------------ Eric Feyfant, Ph.D. Senior research Scientist Computational Chemistry Wyeth Research 200 Cambridge Park Drive Cambridge, MA 02140 tel: +1 617 665 5656 fax: +1 617 665 5682 email: efeyfant@wyeth.com

>>> "Himanshu Grover" hgrover_00@iiita.ac.in 6/30/2004 8:04:44 AM >>>

hi, being a new user, I am facing many problems with modeller. now consider a situation in which i want to model only one particular domain/protein in a protein-protein complex, since the structure for the other domain/protein is available, but then i want to optimize the binding region of the modelled domain taking into context, the other domain as well... is it possible that i use the optimization routine of modeller for the same, only after putting both the proteins of the complex into proper interacting/binding orientation, so that energy minimization can be performed taking into context the entire complex and not just the modelled part thanks, for helping out...

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