Modules
		cctbx.crystal iotbx.crystal_symmetry_from_any iotbx.pdb.crystal_symmetry_from_pdb libtbx.easy_run cctbx.array_family.flex iotbx libtbx mmtbx mmtbx.model_statistics mmtbx.monomer_library os iotbx.pdb random mmtbx.refinement.rigid_body sys mmtbx.utils

Classes
		__builtin__.object fmodel_from_xray_structure modify interpreter   class fmodel_from_xray_structure(__builtin__.object)       Methods defined here: Sorry_high_resolution_is_not_defined(self) __init__(self, xray_structure, f_obs=None, params=None, target_name='ml', r_free_flags_fraction=None, add_sigmas=False) write_to_file(self, file_name) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class interpreter       Methods defined here: __init__(self, command_name, args, log) process_args(self) set_ppf(self)   class modify(__builtin__.object)       Methods defined here: __init__(self, xray_structure, params, all_chain_proxies, log=None) report_number_of_atoms_to_be_removed(self) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)

Functions
		run(args, command_name='phenix.pdbtools') truncate_to_poly_ala(hierarchy)

Data
		fmodel_from_xray_structure_master_params = <libtbx.phil.scope object at 0x355c370> fmodel_from_xray_structure_master_params_str = 'high_resolution = None\n .type = float\nlow_resol...replaced by ".pdbtools.mtz" or ".pdbtools.cns"\n}\n' fmodel_from_xray_structure_params = <libtbx.phil.scope object at 0x34f3b40> fmodel_from_xray_structure_params_str = 'k_sol = 0.0\n .type = float\n .help = Bulk solve...structure factors calculations\n .expert_level=2\n' master_params = <libtbx.phil.scope object at 0x3598758> modify_params = <libtbx.phil.scope object at 0x355cb40> modify_params_str = 'selection = None\n .type = str\n .help = Selecti...pe = int\n .help = Random seed\n .expert_level=2\n'