Protein molecule can be considered on several levels: as a set of chains, a set of residues or as a set of atoms. In BioShell each of these elements is represented by an object i.e. a module that can be used in a script. A protein (i.e. an object of Protein class) is a container for chains. Each chains (object of Chain) is a set of residues. Finally a residue (Residue object) contains atoms (Atom objects)