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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

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

Functions

int main (int argc, char *argv[])
 

Variables

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

using axis = point
using point = numeric::xyzVector<core::Real>
using Pose = core::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
using zinc2_homodimer_setupOP = utility::pointer::shared_ptr<zinc2_homodimer_setup>

Function Documentation

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

Variable Documentation

basic::options::RealOptionKey const angle_rotation_increment("angle_rotation_increment")
basic::options::RealOptionKey const ddG_centroid_cutoff("ddG_centroid_cutoff")
basic::options::StringOptionKey const match1("match1")
basic::options::StringOptionKey const match2("match2")
basic::options::RealOptionKey const tetrahedral_angle_sumsq_cutoff("tetrahedral_angle_sumsq_cutoff")
basic::Tracer TR("apps.pilot.bder.zinc2_homodimer_setup")
static
basic::options::RealOptionKey const zn_zn_distance_cutoff("zn_zn_distance_cutoff")