def exercise_02(): for file_name, input_model in [("m_good.pdb", model_good), ("m_bad.pdb", model_bad)]: tmp_f = open(file_name, "w") tmp_f.write(input_model) tmp_f.close() xrs_exact = iotbx.pdb.pdb_input( file_name="m_good.pdb").xray_structure_simple() model = mmtbx.model.manager(model_input=iotbx.pdb.input( file_name="m_bad.pdb")) xrs_part = model.get_xray_structure() miller_set = miller.build_set( crystal_symmetry=xrs_exact.crystal_symmetry(), anomalous_flag=False, d_min=0.6) f_obs = abs( miller_set.structure_factors_from_scatterers( xray_structure=xrs_exact, algorithm="direct", cos_sin_table=False).f_calc()) sf_par = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract() sf_par.algorithm = "direct" sf_par.cos_sin_table = False fmodel = mmtbx.f_model.manager(xray_structure=xrs_part, sf_and_grads_accuracy_params=sf_par, target_name="ls_wunit_k1", f_obs=f_obs) # out = StringIO() params = find_hydrogens.all_master_params().extract() params.map_cutoff = 6.5 find_hydrogens.run(fmodel=fmodel, model=model, log=out, params=params)
def exercise_02(): for file_name, input_model in [("m_good.pdb", model_good), ("m_bad.pdb", model_bad)]: tmp_f = open(file_name, "w") tmp_f.write(input_model) tmp_f.close() xrs_exact = iotbx.pdb.pdb_input(file_name="m_good.pdb").xray_structure_simple() xrs_part = iotbx.pdb.pdb_input(file_name="m_bad.pdb").xray_structure_simple() miller_set = miller.build_set(crystal_symmetry=xrs_exact.crystal_symmetry(), anomalous_flag=False, d_min=0.6) f_obs = abs( miller_set.structure_factors_from_scatterers( xray_structure=xrs_exact, algorithm="direct", cos_sin_table=False ).f_calc() ) sf_par = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract() sf_par.algorithm = "direct" sf_par.cos_sin_table = False fmodel = mmtbx.f_model.manager( xray_structure=xrs_part, sf_and_grads_accuracy_params=sf_par, target_name="ls_wunit_k1", f_obs=f_obs ) # mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name="m_bad.pdb" ) model = mmtbx.model.manager( xray_structure=xrs_part, pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy, log=None ) # out = StringIO() params = find_hydrogens.all_master_params().extract() params.map_cutoff = 6.5 find_hydrogens.run(fmodel=fmodel, model=model, log=out, params=params)