Usage:
longbond [ -l bond_length | -r bond_ratio ]

Longbond examines each existing bond and removes it if the bond length exceeds a user-specified threshold. This is useful for cleaning up structures with unreasonable bonds, typically resulting from PDB files that lack TER cards or that use ATOM records instead of HETATM records for nonstandard residues.

By default, a bond is removed if its length exceeds 2.5 times its equilibrium length, which is derived from the types of the bonded atoms. The -r flag allows the ratio criterion to be changed from 2.5 to bond_ratio. If the -l flag is given instead, then the bond length is compared against the absolute distance of bond_length rather than a type-dependent distance.