Ensemble Analysis

This module defines classes for handling conformational ensembles.

Conformational ensembles

The following two classes are implemented for handling arbitrary but uniform conformational ensembles, e.g. NMR models, MD snapshots:

• Ensemble
• Conformation

See usage examples in NMR Models and Essential Dynamics Analysis.

PDB ensembles

PDB ensembles, such as multiple structures of the same protein, are in general heterogeneous. This just means that different residues in different structures are missing. The following classes extend above to support this heterogeneity:

• PDBEnsemble
• PDBConformation

The following functions are for creating or editing PDB ensembles, e.g. finding and removing residues that are missing in too many structures:

• buildPDBEnsemble()
• alignByEnsemble()
• calcOccupancies()
• showOccupancies()
• trimPDBEnsemble()

See usage examples in Heterogeneous X-ray Structures, Multimeric Structures, Homologous Proteins.

Save/load ensembles

• saveEnsemble()
• loadEnsemble()