I have a PDB file containing a complex composed of 2 proteins interacting. I wish to perform homology modelling of one of these proteins and leave the other one fixed. I have been able to do the modelling of the one protein of interest, however I am not sure how to have MODELLER include the fixed protein in the final PDB outputs as all my current outputs only contain the modelled protein. Is this some option I can modify on running MODELLER? Or would I have to align the new structures to the old one and somehow merge files to reintroduce the other protein.

Thanks for the help!

Austin