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# 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
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