When we have multiple chains in a model we cannot identify a particular residue without also stating its chain. In essence the residue name must be extended to include the chain name. This is done by combining the chain and residue names by placing a `|' between them. Residue 123 of chain A becomes A|123.
Sometimes a crystal will contain two molecules with the same chemical structure. When this happens we would say that both molecules are of the same type. In TNT each chain has a type. The chain's type defines its amino acid sequence. The RESIDUE statements in the sequence file define the connectivity of a chain type and the type of each chain is defined on the CHAIN statement.
The CHAIN Statement