I'm trying to build a homology model of a multi-chain heteromeric protein (with model-default.py script) using as template a homomeric protein as showed in the following example:
#begin of "ali" file
#End of "ali" file
The model is built normally. However, I noticed that many residues in the active site (which is localized in the interface between each pair of monomers) that are supposed to exposed are turned inside out. I tried to model just as homomeric and so all important side chains in the active site kept the template position. Is there anything I can do to make the modeled residues to adopt the same position as in the template? Would it be reasonable?
I'd appreciate any help!