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Molecule Overview

Overview of the way molecules are stored in the CCPN data model

Below is a schematic view of the 3 levels that we use to handle molecular information:

Molecules as organised in CCPN data model

  • ChemComp: basically contains reference information. The full description of the building blocks for molecules are described on this level (e.g. the atoms, bonds, angles, torsion angles, ... that are present in an alanine amino acid). CCPN provides a large list of reference compounds, but you can define your own.
  • Molecule: this is the template for the molecule. Here you define which 'ChemComp's are present in your molecule, and how they are linked together. You only define each molecule once.
  • MolSystem (Molecular System): basically describes the situation in your sample. So if you want to describe a homotrimer, you only define the component molecule once on the Molecule level. On this level you then create 3 'chains' that each refer back to the same component molecule.