I'm still a bit new to Rosetta. I'm trying to follow the tutorial for comparative modeling here: https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM.
I wonder though if it will work having a template composed of two chains for a target structure that has only one chain. I'm actually stuck trying to align the two strcutures, how can I do that and obtain the alignment in a supported format, for step 1 in the tutorial?
I think it should work if you treat things as a single continuous chain. Just ignore the chainbreak, and concatenate the sequences together. (In the proper order.)
I think that should work without any major alteration of the template PDB, but if worse comes to worse, you can always rename/renumber everything in the template PDB to be the same chain. The partial_threading application won't care about bad geometry at the join (particularly if it's spit up/not aligned to the target sequence), and it's rather agnostic to the naming of the input residues, provided they're in the correct order.