CDR Cluster Constrained Relax Equivalent

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.

Hi Andrew,

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) 

scorefxn.set_weight(dihedral_constraint, 1.0);

modeler.set_scorefunction(scorefxn);

 //Setup Constraints

for cdr in [ l1, l2, l3, h1, h2, h3 ]:

        dih_mover.set_cdr( cdr )
        dih_mover.apply( pose);

  //Run Relax.
 modeler.relax_cdrs(pose, false);