Sorting heteroatoms

The program phenix.sort_hetatms is a utility designed to re-group the non-polymeric molecules (heteroatoms) in a model in a roughly similar manner to the format used by the Protein Data Bank. This consists of matching all heteroatoms to the nearest polymer chain, resetting the chain IDs and residue numbers, converting ATOM labels to HETATM, and optionally sorting waters by B-factor. It is primarily intended or internal use, and is also run within phenix.ligand_pipeline. The only input required is a PDB file, since the program does not deal with molecular geometry or experimental data. Any REMARK records will be removed, but this can be disabled by setting preserve_remarks=True.

Note that the PDB will, inevitably, further modify the contents of the model according to its own rules. However, the program output is significantly closer to the PDB conventions than the output of phenix.refine or similar programs.

List of all available parameters