zinc2_homodimer_setup.cc File Reference

Stage 1 of designing a two-zinc metal seeded symmetric interface. More...

#include <devel/init.hh>
#include <protocols/metal_interface/MatchGrafter.hh>
#include <protocols/metal_interface/MetalSiteResidue.hh>
#include <protocols/metal_interface/ZincSiteFinder.hh>
#include <protocols/analysis/InterfaceAnalyzerMover.hh>
#include <protocols/rigid/RollMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <numeric/conversions.hh>
#include <numeric/xyzVector.hh>
#include <utility/exit.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <sstream>
#include <utility/vector0.hh>

Classes
class	zinc2_homodimer_setup

Typedefs
typedef core::pose::Pose	Pose
typedef numeric::xyzVector < core::Real >	point
typedef point	axis
typedef utility::pointer::shared_ptr < zinc2_homodimer_setup >	zinc2_homodimer_setupOP

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.pilot.bder.zinc2_homodimer_setup")
int	main (int argc, char *argv[])

Variables
basic::options::StringOptionKey const	match1 ("match1")
basic::options::StringOptionKey const	match2 ("match2")
basic::options::RealOptionKey const	angle_rotation_increment ("angle_rotation_increment")
basic::options::RealOptionKey const	ddG_centroid_cutoff ("ddG_centroid_cutoff")
basic::options::RealOptionKey const	zn_zn_distance_cutoff ("zn_zn_distance_cutoff")
basic::options::RealOptionKey const	tetrahedral_angle_sumsq_cutoff ("tetrahedral_angle_sumsq_cutoff")

Detailed Description

Stage 1 of designing a two-zinc metal seeded symmetric interface.

A two-zinc interface is generated in zinc2_homodimer_setup.cc by grafting two 2-residue zinc-binding matches onto the surface, duplicating the pose, rotating 180 degrees about the zinc-zinc axes, then rotating 180 degrees about the line that bisects the two zincs. At this point, there is one significant degree of freedom to exlore WHILE MAINTAINING SYMMETRY. This DOF is rotation about the zinc-zinc axis. The rotation is done in a grid-search manner, and any uneclipsed pose with good metal geometry is dumped/written to disk. The setup is separate from the design to reduce the computational load, and to provide a debugging checkpoint.

This protocol is for two zincs at the interface. I wrote a similar protocol for designing symmetric interfaces containing only one zinc, but none of these designs worked experimentally.

Typedef Documentation

typedef point axis

typedef numeric::xyzVector<core::Real> point

typedef core::pose::Pose Pose

Chain1Chain1Chain1 H H H H H-H match1, H-H match2 \ / \ / Zn Zn -------------—— axis of symmetry, can rotate about this axis and maintain symmetry / \ / \ H H H H H-H match2, H-H match1 Chain2Chain2Chain2

Author

Bryan Der

typedef utility::pointer::shared_ptr< zinc2_homodimer_setup > zinc2_homodimer_setupOP

Function Documentation

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

References angle_rotation_increment, utility::io::oc::cout, ddG_centroid_cutoff, devel::init(), match1, match2, utility::excn::EXCN_Base::msg(), basic::options::option, option, tetrahedral_angle_sumsq_cutoff, TR(), and zn_zn_distance_cutoff.

static THREAD_LOCAL basic::Tracer TR ( "apps.pilot.bder.zinc2_homodimer_setup"  )

static

Referenced by zinc2_homodimer_setup::apply(), zinc2_homodimer_setup::filter_clashes(), zinc2_homodimer_setup::filter_metal_geom(), main(), zinc2_homodimer_setup::setup_grafted_monomer(), zinc2_homodimer_setup::setup_homodimer(), zinc2_homodimer_setup::setup_metalsites(), and zinc2_homodimer_setup::zinc2_homodimer_setup().

Variable Documentation

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

Referenced by zinc2_homodimer_setup::gridsearch_symmetric_alignments(), and main().

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

Referenced by zinc2_homodimer_setup::filter_clashes(), and main().

basic::options::StringOptionKey const match1("match1")

Referenced by main(), and zinc2_homodimer_setup::zinc2_homodimer_setup().

basic::options::StringOptionKey const match2("match2")

Referenced by main(), and zinc2_homodimer_setup::zinc2_homodimer_setup().

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

Referenced by zinc2_homodimer_setup::filter_metal_geom(), and main().

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

Referenced by zinc2_homodimer_setup::filter_clashes(), and main().