Molecular Replacement with multiple chains

Hi all,

I am trying to use the Molecular Replacement functions of Rosetta (mr_protocols), and all seems to work well as I go through the example.

However, I am trying to solve the structure of a protein with two chains, and I am getting confused on how to handle this with the alignment files. For instance, I have grabbed the hhr files from the HHpred server, but I can only submit a single chain at a time.

Is there a way to combine the hhr files for each chain, so that I can use it with mr_protocols???

Any advice would be appreciated. I am at a complete loss here.

Many thanks,
Brett