I have a protein and I am only interested in modeling two parts of it, constraining the rest of the protein to the structure that we already know. I am new to Rosetta and would like to know what the best approach to this would be.
I am assuming that homology modeling is the way to go and have studied the tutorial, but without constraining the well defined part of the protein I am afraid that it will be impossible to produce a model that will be of structural significance. Could anyone assist me what the best way to set those constraints would be ( essentially just freezing the parts that we are not interested in modelling but I still want them to be there so that the parts of the protein that I am interested in are linked to the rest of the chain sensibly).
Thank you for any inout in advance
If you use the RosettaCM protocol, it should *heavily* rely on the structures from the templates, where there's good alignment. So what you want to do is use the existing structure as the (only) template for the regions which are "fixed", and use standard alignments for those regions you wish to model with homology.
That won't keep things absolutely fixed, but normally you'll want some flexibility anyway. Standard homology modeling should result in relatively decent results.
If you get too much flexibility in the known regions, you can always add additional constraints (e.g. atom pair constraints) in the regions which show high flexibility. But honestly, that's unlikely to be the case, so I'd recommend doing it without first.