Looking through the doucmentation, I found references to an application called "relax_cdrs", which enables relaxation of CDRs with constraints derived from their corresponding CDR cluster. (link to documentaiton below).
I've looked through recent weekly releases, but I can't find this binary. Can somone point me to the source file for this protocol, or some equivalent that would enable me to do the same thing? Alternatively, an explanation of how to do this in pyrosetta would be even better.
It was never released (the file is still at ./source/src/apps/pilot/jadolfbr/cluster_utilities/relax_cdrs.cc; the pilot directory is stripped from the releases). You haven't failed to find it - it's just not there yet. I'll make sure Jared's aware of your interest and fix its documentation.
This application was not yet ready for release, but since there is documentation for it and interest, I will make it available in the next weekly release.
To do it in PyRosetta, you will need to setup a few things, all should be accessible. Let us know if you try it and something here doesn't work:
Note that the antibody design modeler will allow you set which CDRs you want to relax (default is all of them) (modeler.set_cdr), as well as an overhang (modeler.set_cdr_overhang), which denotes how many residues you want to model going into the antibody framework.
from rosetta.protocols.antibody import *
from rosetta.protocols.antibody.design import *
from rosetta.protocols.antibody.constraints import *
ab_info = AntibodyInfo(pose, AHO_Scheme, North); #If your antibody is in AHO and you would like to use North CDR definitions. See the general antibody info for more.
dih_mover = CDRDihedralConstraintMover(ab_info)
modeler = GeneralAntibodyModeler(ab_info);
scorefxn = get_score_function(true)
for cdr in [ l1, l2, l3, h1, h2, h3 ]:
dih_mover.set_cdr( cdr )
I just downloaded the latest weekly release (June 12th, rosetta_bin_linux_2016.18.58680_bundle), but the application doesn't appear to be present (I also can't find the source file relax_cdrs.cc either). Any chance you could email that source file?
I haven't been able to check out the pyrosetta protocol yet (having trouble compiling from source), but will try once I get it to compile.