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IMP Reference Guide  develop.374319d7bb,2024/06/17
The Integrative Modeling Platform
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...