- convert_semet_to_met(pdb_hierarchy, xray_structure)
- Change the chemical identity of MSE residues to MET, without changing
- move_waters(pdb_hierarchy, xray_structure, out)
- Re-arranges the PDB hierarchy so that waters are located at the end of the
atom list. This is done automatically in phenix.refine if water picking is
enabled, but the routine here is more flexible. (Note that there is some
overlap in functionality with mmtbx.command_line.sort_hetatms, but the
latter module is significantly more complicated.)
- normalize_occupancies(hierarchy, selection=None, xray_structure=None, log=None)
- Reset the sum of occupancies for each residue_group to 1.0. This will fail
if any (selected) atom_group has non-uniform occupancies.
- remove_alt_confs(hierarchy, always_keep_one_conformer=False)
- Remove all alternate conformers from the hierarchy. Depending on the
value of always_keep_one_conformer, this will either remove any atom_group
with altloc other than blank or 'A', or it will remove any atom_group
beyond the first conformer found.
- rename_chain_id(hierarchy, params, log)
- renumber_residues(pdb_hierarchy, renumber_from=None, atom_selection=None, log=None)
- run(args, command_name='phenix.pdbtools', out=<open file '<stdout>', mode 'w'>, replace_stderr=True)
- set_atomic_charge(hierarchy, xray_structure, pdb_atoms, selection, charge, log=None)
- Set the charge for selected atoms. Note that both the hierarchy and the
xray_structure must be passed here - in the context of the pdbtools app,
the scattering_type attributes will override the atom's element and charge
when the structure is written out.
- Remove all protein sidechain atoms beyond C-alpha (as well as all hydrogens).
Does not change the chemical identity of the residues.
- validate_params(params, callback=None)
- write_model_file(pdb_hierarchy, crystal_symmetry, file_name, output_format)