Is there a Rosetta script/scenario to perform a partial ab initio model? I mean, I am working with a protein sequence which has two structural subdomains already solved and available in two separate PDB's. The sequence I'm working on spans the two subdomains and has additional parts, which have not been solved and have poor SS predictions. I was thinking of using a Rosetta scenario/script to model the C- and N-terminal of the sequence and the linker between these two subdomains while keeping their original structures. The problem is, the relative position between these structural subdomains is unknown.
Does the script "thread_pdb_from_alignment.py" support a multiple sequence alignments and multiple pdb templates?
Please, could someone shed some light on this problem?