I know the full amino acid sequence for my protein. I have obtained its X-ray crystal PDB structure, as well as the mtz file from the crystallisation. There are several loops and termini not resolved. Can I ask what is the best protocol to predict the missing part? I understand it would still not be fully "true" after Rosetta's modelling. I just want to have a "mostly likely" one that can be used as the starting point for my molecular dynamic simulation.
I have been told remodel is used for "design", not "predict", so not applicable to predict the missing structures.
It seems that homology modelling (e.g. RosettaCM) is recommended.
(Maybe this thread is just for a general discussion about the possible protocols available.)