IMP.pmi.restraints.npc Namespace Reference

Specialized restraints for modeling the Nuclear Pore Complex. More...

Detailed Description

Specialized restraints for modeling the Nuclear Pore Complex.

These restraints have been used to model the Nuclear Pore Complex (NPC) but may be useful for other applications too. They model the NPC as lying in the xy plane, centered at the origin. (Transport through the pore corresponds to movement along the z axis.) The surface of the nuclear membrane is represented as the surface of a half torus, also lying in the xy plane and centered at the origin. Individual proteins (or parts of proteins, such as the N- or C- termini) are then localized to different regions of the complex (e.g. near the membrane or pore, or on the nuclear or cytoplasmic side) by simple restraints on their Cartesian coordinates.

Classes
class	MembraneExclusionRestraint
	Keep protein away from a half torus in the xy plane. More...
class	MembraneSurfaceLocationConditionalRestraint
	Localize one protein on the surface of a half torus in the xy plane. More...
class	MembraneSurfaceLocationRestraint
	Localize protein on the surface of a half torus in the xy plane. More...
class	XYRadialPositionLowerRestraint
	Restrain a protein's distance from the z axis to above a lower bound. More...
class	XYRadialPositionRestraint
	Restrain a protein's distance from the z axis to within a given range. More...
class	XYRadialPositionUpperRestraint
	Restrain a protein's distance from the z axis to below an upper bound. More...
class	YAxialPositionLowerRestraint
	Restrain a protein's y coordinate to above a lower bound. More...
class	YAxialPositionRestraint
	Restrain a protein's y coordinate to within a given range. More...
class	YAxialPositionUpperRestraint
	Restrain a protein's y coordinate to below an upper bound. More...
class	ZAxialPositionLowerRestraint
	Restrain a protein's z coordinate to above a lower bound. More...
class	ZAxialPositionRestraint
	Restrain a protein's z coordinate to within a given range. More...
class	ZAxialPositionUpperRestraint
	Restrain a protein's z coordinate to below an upper bound. More...