On 12/4/20 9:08 AM, shivu shiv wrote:
> 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.

If you are confident of this orientation, put the two chains in a single
PDB file, as is done in the example in the manual:
https://salilab.org/modeller/9.25/manual/node29.html

Modeller extracts internal distance restraints from each template
separately, so if your two chains are two separate templates, there will
be no inter-chain restraints.

        Ben Webb, Modeller Caretaker
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