These chains themselves contain one or more groups of atoms. Each group is either one of 20 amino acids or 5 nucleosides. Each atom, regardless of whether it is standard or non-standard, contains its own line in the PDB file. Chain, space-filled rendering of a PDB DNA molecule. Amino group, bond only rendering of a PDB DNA molecule.
Implicit bonds occur between standard atoms in the same group.
The MOL File Format MOL is a more general format, designed to convey all types of molecules. The format contains similar information to that of a PDB file, but it lacks chain and group information, since that does not apply to a general molecule. Properly interpret chains, groups and their interconnecting bonds, i.e. Sugar Phosphates, Polypeptide Chains and Disulphide Bridges Organize atoms into folders based on their group and chain ids. Display an increased volume, Space Filled, representation where bonds are shown by atoms overlapping. Set the coloring scheme for an atom based on its element, its parent model, its parent chain or its group type.