Structures and ensembles

A typical task in Analysis is to connect NMR signals to atoms in molecules. Often, especially at the start phase of a structure determination, no information is available about the 3-dimensional structure of the molecule, and one can only connect NMR information to atoms on the level of the molecular topology without any structure coordinate information. This molecular topology can be defined and added to a Molecular System, which allows the user to connect NMR information to molecular information (See also Molecules).

However, when structural information is available, for example after initial structure calculations or from structures deposited at the PDB, it is important that the NMR information can be directly linked to the 3D structure models to expand the number of analysis possibilities. For this CcpNmr Analysis uses the concept of structures and ensembles, where an ensemble is a group of structure models (Figure 1).

Figure 1. An ensemble is a group of structural models.

Using structures and ensembles in Analysis

In Analysis, an ensemble consisting of several structures can be imported and exported to and from e.g. a PDB file. Any structures present within a CCPN project will be saved along with that project, so no special attention is needed to write the information to disk. Both the ensemble and the structures can be analysed separately. Ensembles can be split into separate models, and models can be merged into ensembles. Analysis also has a built in structure viewer, with some basic functionality for displaying and changing the view of structures. A useful feature in Analysis is that you can use it to directly display the NMR data on a structure, for example NOE distance restraints or chemical shifts.

Connecting structures with peaks and assignments

To display and analyse connections between structure coordinates and NMR data, the atoms in the structures and ensembles need to be connected to the molecular system in which the assignments are made. Technically, this is done in the package MolStructure of the CCPN data model, in which coordinates are stored. This package has to be synchronized with the MolSystem package in terms of chains, residues and atoms to make the correct connections. Therefore when a structure ensemble is loaded, it is mandatory to specify which Molecular System the ensemble relates to, and it is only the atoms of this Molecular System that the imported structure ensemble may specify coordinates for. Once this has been done correctly, it becomes possible to e.g. navigate from atoms in a structure to the peaks that are assigned to these atoms.

Figure 2. The molecular system and the molecular structure can after a structure calculation be synchronized so that the atom coordinates are connected to the atom assignments.

Structures and ensembles