I am working on modeling a protein with two chains (heterodimer). 

I have used two separate pdb files for each chain and oriented the two template structures appropriately before the modeling.

Modeller is able to model both the chains, however not preserving the orientation of both the chains. 

I am seeking suggestions for how to specify restraints to preserve the orientation of both the chains with respect to each other. Please provide your suggestions.

Thanks and Regards

shivu