Contents of the PDB Output File

The output.pdb written by CHAP reproduces the structure contained in the topology (the input passed to CHAP with the -s flag), but overwrites the occupancy and temperature factor fields of each ATOM record with values indicating whether an atom belongs to a residue that is considered pore-lining and pore-facing respectively.

To be precise, both fields contain a number between zero and one that indicates the fraction of time a residue was considered pore-lining or pore-facing respectively, where a value of one means that a residue has been pore-lining (or pore-facing) for every frame in the input trajectory, while a value of zero indicates that a residue has never been found to be pore-lining (or pore-facing). As the pore-lining and pore-facing attributes are calculated on a per-residues basis, this number will be identical for all atoms of the same residue.