Further reading about structures and ensembles

Structures and ensembles in the CcpNmr Analysis Data model

The MolStructure package is divided in several objects that all contain different information related to the structures and ensembles (See Figure 1). The objects involved are as follows:

StructureEnsemble - This is the 'top' object of the package and contains all of the structures. A StructureEnsemble represents what you would find in the body of a PDB file; It is a set of atomic coordinates that go together to describe the conformation of a molecule. The StructureEnsemble might contain several models, which represent alternative conformations, but these are always for the same set of atoms. A StructureEnsemble belongs to a CCPN project and is identified by an identifier (ID) and a MolSystem. Thus it is mandatory to specify which MolSystem a StructureEnsemble relates to, when it is created and it is only the atoms of this MolSystem that the StructureEnsemble may specify coordinates for. Each StructureEnsemble has its own directory which it is stored, which makes it possible to load structures independently from one another.

Chain -This object belongs to a StructureEnsemble and is a container for the structure's Residues. The Chains here are always linked to the Chains in the MolSystem. However, there need not to be a “MolStructure Chain” for every “MolSystem Chain”; for example you may have a protein which you just have started to assign so the structure is not yet available.

Residue - Residue belongs to a Chain and acts as a container for structural atoms. A Residue may be missing in the Chain, even if the residue is present in the MolSystem package. In this way can the MolStructure package only partly be linked to the MolSystem package.

Atom -These structural atoms belong to the structure's residues, and link to equivalent atoms in the ensemble's MolSystem. An Atom may contain several coordinate records which specify the atom's position in different conformations, and in this case each of the coordinates represent a different model.

Coord -This is the coordinate record which belongs to a given atom in a given model. It specifies an atomic location in cartesian (x,y,z) coordinates and carries records of B-factor etc. 

Model -The Model object belongs to the top-level StructureEnsemble object and serves to group coordinates together which relate to the same molecular conformation. Sometimes there will only be one Model and one set of coordinates. If the structure only has one conformation there will be only one Model, i.e. one set of coordinates, but if the structure represents an ensemble of conformations then there will be many Models.

Figure 1. Each Chain, Residue and Atom object in the MolStructure package can be linked to equivalent objects in the MolSystem package. The Atom object stores coordinate information (Coord) for each model in the StructureEnsemble.