# This is an example of how to use constrainInterfaces to do template-based docking.
# See our paper, Dourado and Flores, Nat. Sci. Reports 2016 (doi:10.1038/srep25406)

# This example is a bit trivial, in that we are bringing chain A in to replace chain C. But chain A and chain C are actually identical.  But this should give you the idea.


firstStage 2
lastStage 3


# Make sure these PDB files are in the current directory, of course:
loadSequencesFromPdb 1FC2.pdb
# This contains a chain C which has been renamed "A".  chain D is deleted:
loadSequencesFromPdb 1FC2.C-to-A.pdb

readAtStage 2
# Just for illustration, we start with the new chain (A) displaced away from the Fc (D):
initialDisplacement A 10 0 0
# Now we pull A onto C:
alignmentForces A C   
# Note we do not have to provide residue numbers, a gapped threading will take care of that.

# While keeping C (original SpA) on Fc (D):
constrainInterfaces .6  
# This command detects any clashes. Note A and C clash later in the stage!  This is expected, and is not a problem, particularly since physics is turned off.
detectInterChainClashes .1
readBlockEnd

mobilizer Rigid




readAtStage 3
# Now we move the original chain (C) out of the picture:
initialDisplacement C 10 0 0
# And constrain the new chain A to the Fc (D):
constrainInterfaces .6 
readBlockEnd