def exercise_2(): """ Same as 1 but automatic NCS search procedure does not match short chains, in this case chains B,C, so they left out of NCS. Not clear if we should utilize MTRIX instead of searching for NCS because currently we don't output them and in consecutive runs NCS search would be utilized anyway, potentially yelding different groups. """ inp = iotbx.pdb.input(source_info=None, lines=pdb_str_2) pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params( ) pdb_int_params.pdb_interpretation.ncs_search.enabled = True model = mmtbx.model.manager(model_input=inp, pdb_interpretation_params=pdb_int_params, process_input=True, log=null_out()) # model.get_xray_structure() ss = model.get_ss_annotation() assert ss.get_n_helices() == 3 assert ss.get_n_sheets() == 3 assert not model.ncs_constraints_present() assert model.get_ncs_obj() is not None model.setup_ncs_constraints_groups() # print model.get_ncs_obj() assert model.ncs_constraints_present() assert model.get_master_hierarchy().atoms_size() == 15 # print model.get_master_hierarchy().as_pdb_string() assert list(model.get_master_selection()).count(True) == 15
def test_2(): inp = iotbx.pdb.input(source_info=None, lines=pdb_str_0) model = mmtbx.model.manager(model_input=inp) model.expand_with_BIOMT_records() model = shift_and_box_model(model) model.search_for_ncs() model.setup_ncs_constraints_groups(filter_groups=True) assert model.ncs_constraints_present() assert not model.can_be_unique_with_biomt() assert "" == model.model_as_mmcif(try_unique_with_biomt=True)
def exercise_1(): inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1) model = mmtbx.model.manager( model_input = inp, log = null_out()) assert model.get_number_of_atoms() == 21 assert model.get_hierarchy().atoms_size() == 21 assert model.get_xray_structure().scatterers().size() == 21 ss = model.get_ss_annotation() # print ss.as_pdb_str() # STOP() assert ss.get_n_helices() == 3 # because the second strand contains chain B which is not in ATOM records # whole sheet got discarded. assert ss.get_n_sheets() == 0 rm = model.get_restraints_manager() assert rm.geometry.pair_proxies().bond_proxies.simple.size() == 6 # since No NCS was set, these functions return the whole thing and no # master selection assert model.get_master_hierarchy().atoms_size() == 21 assert model.get_master_selection().size() == 0 # print model.model_as_pdb() # print "="*40 # Here we set NCS constraints inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1) pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params() pdb_int_params.pdb_interpretation.ncs_search.enabled=True model = mmtbx.model.manager( model_input = inp, pdb_interpretation_params = pdb_int_params, process_input=True, log = null_out()) # model.get_xray_structure() assert not model.ncs_constraints_present() assert model.get_ncs_obj() is not None model.setup_ncs_constraints_groups() # print model.get_ncs_obj() assert model.ncs_constraints_present() assert model.get_master_hierarchy().atoms_size() == 7 # print model.get_master_hierarchy().as_pdb_string() # print list(model.get_master_selection()) assert list(model.get_master_selection()).count(True) == 7
def test_1(): inp = iotbx.pdb.input(source_info=None, lines=pdb_str_0) model = mmtbx.model.manager(model_input=inp) model.expand_with_BIOMT_records() model = shift_and_box_model(model) sel = model.selection("chain '0' or chain 'C' or chain 'F' or chain 'I' or chain 'L' or chain 'O' or chain 'R' or chain 'U' or chain 'X'") model = model.select(sel) model.search_for_ncs() model.setup_ncs_constraints_groups(filter_groups=True) n1 = model.get_number_of_atoms() assert n1 == 648, n1 assert model.ncs_constraints_present() nrgl = model.get_ncs_groups() assert len(nrgl[0].master_iselection) == 72 assert len(nrgl[0].copies) == 8 # nrgl._show() # print (model.can_be_unique_with_biomt()) cif_txt = model.model_as_mmcif(try_unique_with_biomt=True) # print (cif_txt) assert_lines_in_text(cif_txt, """ loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 (1-9) A""") assert_lines_in_text(cif_txt, """ loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'Symmetry assembly' ? ? ? """) assert_lines_in_text(cif_txt, """ _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'point symmetry operation' ? ? 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0""") inp = iotbx.pdb.input(source_info=None, lines=cif_txt) m2 = mmtbx.model.manager(model_input=inp) n2_1 = m2.get_number_of_atoms() assert n2_1 == 72 m2.expand_with_BIOMT_records() n2_2 = m2.get_number_of_atoms() # print (n1, n2) assert n1 == n2_2, "%d, %d" % (n1, n2)
def __init__(self, model, target_map, refine_ncs_operators=False, number_of_cycles=1, cycles_to_converge=2, log=None): # completely new way of doing this. using RSR macro-cycle # for test compatibility: print("Minimizing using reference map...", file=log) if model.ncs_constraints_present(): print(" Minimizing... (NCS)", file=log) else: print(" Minimizing...", file=log) from phenix.refinement.macro_cycle_real_space import run as rsr_mc_run import scitbx.math from phenix.command_line.real_space_refine import extract_rigid_body_selections from phenix.command_line.real_space_refine import master_params as rsr_master_params from mmtbx.refinement.real_space.utils import target_map as rsr_target_map import mmtbx.idealized_aa_residues.rotamer_manager sin_cos_table = scitbx.math.sin_cos_table(n=10000) params = rsr_master_params().extract() params.pdb_interpretation = model._pdb_interpretation_params.pdb_interpretation params.refinement.run = "minimization_global+local_grid_search" params.refine_ncs_operators = False params.output.write_all_states = True rotamer_manager = mmtbx.idealized_aa_residues.rotamer_manager.load( rotamers="favored") rigid_body_selections = extract_rigid_body_selections( params=params, ncs_groups=model.get_ncs_groups(), pdb_hierarchy=model.get_hierarchy()) rsr_tm = rsr_target_map(map_data=target_map, xray_structure=model.get_xray_structure(), d_min=3.8, atom_radius=params.refinement.atom_radius) res = rsr_mc_run(params=params, model=model, target_map=rsr_tm, log=log, ncs_groups=model.get_ncs_groups(), rotamer_manager=rotamer_manager, sin_cos_table=sin_cos_table, rigid_body_selections=rigid_body_selections) model.set_sites_cart_from_hierarchy(res.model.get_hierarchy()) res.structure_monitor.states_collector.write( file_name="rsr_all_states.pdb") return # end =================================================== from mmtbx.refinement.geometry_minimization import add_rotamer_restraints from mmtbx.refinement.minimization_monitor import minimization_monitor self.model = model self.log = log print("Minimizing using reference map...", file=self.log) self.log.flush() # copy-paste from cctbx_project/mmtbx/refinement/geometry_minimization.py: # minimize_wrapper_for_ramachandran self.model.get_restraints_manager().geometry.pair_proxies( sites_cart=self.model.get_sites_cart()) ncs_restraints_group_list = self.model.get_ncs_groups() if ncs_restraints_group_list is None: ncs_restraints_group_list = [] ncs_groups = None if len(ncs_restraints_group_list) > 0: ncs_groups = ncs_restraints_group_list min_monitor = minimization_monitor( number_of_cycles=number_of_cycles, max_number_of_cycles=20, cycles_to_converge=cycles_to_converge, mode="no_outliers") selection_real_space = None import mmtbx.refinement.real_space.weight self.w = 1 print("number_of_cycles", number_of_cycles, file=log) print("Stats before minimization:", file=log) ms = self.model.geometry_statistics() ms.show(log=log) while min_monitor.need_more_cycles(): print("Cycle number", min_monitor.get_current_cycle_n(), file=self.log) self.model.get_restraints_manager().geometry.\ update_ramachandran_restraints_phi_psi_targets( hierarchy=self.model.get_hierarchy()) print(" Updating rotamer restraints...", file=self.log) add_rotamer_restraints( pdb_hierarchy=self.model.get_hierarchy(), restraints_manager=self.model.get_restraints_manager(), selection=None, sigma=5, mode="fix_outliers", accept_allowed=False, mon_lib_srv=self.model.get_mon_lib_srv(), rotamer_manager=self.model.get_rotamer_manager()) self.model.set_sites_cart_from_hierarchy() if min_monitor.need_weight_optimization(): # if self.w is None: print(" Determining weight...", file=self.log) self.log.flush() self.weight = mmtbx.refinement.real_space.weight.run( map_data=target_map, xray_structure=self.model.get_xray_structure(), pdb_hierarchy=self.model.get_hierarchy(), geometry_restraints_manager=self.model. get_restraints_manager(), rms_bonds_limit=0.015, rms_angles_limit=1.0, ncs_groups=ncs_groups) # division is to put more weight onto restraints. Checked. Works. self.w = self.weight.weight / 3.0 # self.w = self.weight.weight/15.0 # self.w = 0 # self.w = self.weight.weight for s in self.weight.msg_strings: print(s, file=self.log) if ncs_restraints_group_list is None or len( ncs_restraints_group_list) == 0: #No NCS print(" Minimizing...", file=self.log) print(" with weight %f" % self.w, file=self.log) self.log.flush() refine_object = simple( target_map=target_map, selection=None, max_iterations=150, geometry_restraints_manager=self.model. get_restraints_manager().geometry, selection_real_space=selection_real_space, states_accumulator=None, ncs_groups=ncs_groups) refine_object.refine( weight=self.w, xray_structure=self.model.get_xray_structure()) self.rmsd_bonds_final, self.rmsd_angles_final = refine_object.rmsds( ) print("RMSDS:", self.rmsd_bonds_final, self.rmsd_angles_final, file=log) # print >> log, "sizes:", len(refine_object.sites_cart()), len(self.xrs.scatterers()) self.model.set_sites_cart(refine_object.sites_cart(), update_grm=True) # print >> log, "sizes", self.xrs.scatterers() else: # Yes NCS # copy-paste from macro_cycle_real_space.py # !!! Don't rearrange NCS groups here because master was just fixed! # import mmtbx.ncs.ncs_utils as nu # nu.get_list_of_best_ncs_copy_map_correlation( # ncs_groups = ncs_restraints_group_list, # xray_structure = self.model.get_xray_structure(), # map_data = target_map, # d_min = 3) print(" Minimizing... (NCS)", file=self.log) tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\ target_function_and_grads_real_space( map_data = target_map, xray_structure = self.model.get_xray_structure(), ncs_restraints_group_list = ncs_restraints_group_list, refine_selection = None, real_space_gradients_delta = 1, restraints_manager = self.model.get_restraints_manager(), data_weight = self.w, refine_sites = True) minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( target_and_grads_object=tfg_obj, xray_structure=self.model.get_xray_structure(), ncs_restraints_group_list=ncs_restraints_group_list, refine_selection=None, finite_grad_differences_test=False, max_iterations=100, refine_sites=True) self.model.set_sites_cart(tfg_obj.xray_structure.sites_cart()) ncs_restraints_group_list.recalculate_ncs_transforms( self.model.get_sites_cart()) ms = self.model.geometry_statistics() min_monitor.save_cycle_results(geometry=ms) ms.show(log=log)