Starts with an undesigned symmetric dimer with two interface zinc sites as created by zinc2_homodimer_design_setup, and designs the interface with sc, bb, and jump minimization. More...

#include <devel/init.hh>
#include <protocols/metal_interface/MetalSiteResidue.hh>
#include <protocols/metal_interface/ZincSiteFinder.hh>
#include <protocols/metal_interface/AddZincSiteConstraints.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/task_operations/RestrictToInterfaceOperation.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <numeric/xyzVector.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <protocols/symmetry/SetupForSymmetryMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.fwd.hh>
#include <protocols/minimization_packing/MinMover.fwd.hh>
#include <sstream>
#include <core/conformation/Residue.hh>

Classes
class	zinc2_homodimer_design

Typedefs
using	point = numeric::xyzVector< core::Real >

using	axis = point

using	Pose = core::pose::Pose

using	zinc2_homodimer_designOP = utility::pointer::shared_ptr< zinc2_homodimer_design >

Functions
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.bder.zinc2_homodimer_design")

basic::options::IntegerOptionKey const	repackmin_iterations ("repackmin_iterations")

basic::options::RealOptionKey const	fav_nat_bonus ("fav_nat_bonus")

basic::options::IntegerOptionKey const	nstruct_iterations ("nstruct_iterations")

Detailed Description

Starts with an undesigned symmetric dimer with two interface zinc sites as created by zinc2_homodimer_design_setup, and designs the interface with sc, bb, and jump minimization.

Prior to running this protocol, 'make_NCS.pl' must be applied to the symmetric zinc dimer to define the symmetry. The consequence is that the input PDB is actually the monomer generated by 'make_NCS.pl' along with the symmetry definition file. Reconstituting the dimer is the first step in this protocol. Next, the metal binding sites are located, an appropriate taskfactory, movemaps, and movers are setup, and finally the dimer is iteratively designed with packrotamers and minimization. Constraints are applied to the two metal sites, allowing minimization while respecting metal coordination geometry.