from __future__ import absolute_import, division, print_function import mmtbx.monomer_library.pdb_interpretation import iotbx.mtz from cctbx.array_family import flex import time from mmtbx import monomer_library import iotbx.pdb import sys import mmtbx.refinement.real_space.fit_water pdb_answer = """\ CRYST1 29.709 30.639 28.034 90.00 90.00 90.00 P 1 ATOM 1 CB MET A 1 11.971 15.000 12.927 1.00 10.00 A C ATOM 2 CG MET A 1 12.074 15.930 14.126 1.00 10.00 A C ATOM 3 SD MET A 1 12.820 17.522 13.722 1.00 10.00 A S ATOM 4 CE MET A 1 14.460 17.016 13.210 1.00 10.00 A C ATOM 5 C MET A 1 11.191 12.831 11.962 1.00 10.00 A C ATOM 6 O MET A 1 12.202 12.489 11.349 1.00 10.00 A O ATOM 7 CA MET A 1 11.294 13.663 13.235 1.00 10.00 A C ATOM 8 N MET A 1 12.057 12.926 14.282 1.00 10.00 A N ATOM 9 D1 MET A 1 11.949 13.331 15.067 1.00 10.00 A D ATOM 10 D2 MET A 1 11.756 12.090 14.335 1.00 10.00 A D ATOM 11 D3 MET A 1 12.921 12.918 14.068 1.00 10.00 A D ATOM 12 DA MET A 1 10.401 13.848 13.565 1.00 10.00 A D ATOM 13 DB2 MET A 1 12.870 14.826 12.608 1.00 10.00 A D ATOM 14 DB3 MET A 1 11.461 15.457 12.240 1.00 10.00 A D ATOM 15 DG2 MET A 1 11.184 16.097 14.473 1.00 10.00 A D ATOM 16 DG3 MET A 1 12.621 15.508 14.806 1.00 10.00 A D ATOM 17 DE1 MET A 1 15.002 17.807 13.062 1.00 10.00 A D ATOM 18 DE2 MET A 1 14.854 16.470 13.909 1.00 10.00 A D ATOM 19 DE3 MET A 1 14.391 16.504 12.389 1.00 10.00 A D TER 20 MET A 1 ATOM 23 O HOH S 2 16.264 14.181 13.359 1.00 10.00 A O ATOM 24 D1 HOH S 2 16.839 14.787 13.448 1.00 10.00 A D ATOM 25 D2 HOH S 2 15.607 14.525 12.964 1.00 10.00 A D ATOM 26 O HOH S 3 12.726 17.501 10.452 1.00 10.00 A O ATOM 27 D1 HOH S 3 13.400 18.002 10.452 1.00 10.00 A D ATOM 28 D2 HOH S 3 12.051 18.001 10.452 1.00 10.00 A D ATOM 29 O HOH S 4 15.741 14.515 10.999 1.00 10.00 A O ATOM 30 D1 HOH S 4 16.265 14.645 10.355 1.00 10.00 A D ATOM 31 D2 HOH S 4 15.049 14.965 10.844 1.00 10.00 A D ATOM 32 O HOH S 5 14.953 14.255 15.525 1.00 10.00 A O ATOM 33 D1 HOH S 5 15.650 14.629 15.243 1.00 10.00 A D ATOM 34 D2 HOH S 5 14.518 14.838 15.946 1.00 10.00 A D ATOM 35 O HOH S 6 16.821 13.421 16.856 1.00 10.00 A O ATOM 36 D1 HOH S 6 17.631 13.624 16.944 1.00 10.00 A D ATOM 37 D2 HOH S 6 16.377 14.028 17.230 1.00 10.00 A D ATOM 38 O HOH S 7 14.155 17.061 16.899 1.00 10.00 A O ATOM 39 D1 HOH S 7 14.829 17.562 16.899 1.00 10.00 A D ATOM 40 D2 HOH S 7 13.480 17.561 16.899 1.00 10.00 A D ATOM 41 O HOH S 8 13.608 20.138 14.103 1.00 10.00 A O ATOM 42 D1 HOH S 8 14.282 20.639 14.103 1.00 10.00 A D ATOM 43 D2 HOH S 8 12.933 20.638 14.103 1.00 10.00 A D ATOM 44 O HOH S 9 19.039 15.775 13.706 1.00 10.00 A O ATOM 45 D1 HOH S 9 19.709 16.282 13.708 1.00 10.00 A D ATOM 46 D2 HOH S 9 18.362 16.267 13.776 1.00 10.00 A D ATOM 59 O HOH S 14 14.398 12.604 10.286 1.00 10.00 A O ATOM 60 D1 HOH S 14 15.141 12.872 10.000 1.00 10.00 A D ATOM 61 D2 HOH S 14 13.834 13.195 10.088 1.00 10.00 A D ATOM 62 O HOH S 15 14.467 12.610 12.855 1.00 10.00 A O ATOM 63 D1 HOH S 15 15.185 12.287 12.563 1.00 10.00 A D ATOM 64 D2 HOH S 15 14.064 12.942 12.196 1.00 10.00 A D ATOM 65 O HOH S 16 14.507 11.895 15.986 1.00 10.00 A O ATOM 66 D1 HOH S 16 15.110 12.251 16.450 1.00 10.00 A D ATOM 67 D2 HOH S 16 13.801 12.325 16.133 1.00 10.00 A D ATOM 68 O HOH S 17 13.717 10.000 14.614 1.00 10.00 A O ATOM 69 D1 HOH S 17 14.356 10.543 14.556 1.00 10.00 A D ATOM 70 D2 HOH S 17 13.019 10.457 14.711 1.00 10.00 A D ATOM 71 O HOH S 18 13.592 14.007 17.533 1.00 10.00 A O ATOM 72 D1 HOH S 18 14.264 13.943 18.034 1.00 10.00 A D ATOM 73 D2 HOH S 18 12.988 14.378 17.983 1.00 10.00 A D ATOM 74 O HOH S 19 16.563 12.061 14.539 1.00 10.00 A O ATOM 75 D1 HOH S 19 17.279 12.499 14.505 1.00 10.00 A D ATOM 76 D2 HOH S 19 15.937 12.621 14.553 1.00 10.00 A D TER 63 HOH S 19 END """ pdb_poor = """\ CRYST1 29.709 30.639 28.034 90.00 90.00 90.00 P 1 ATOM 1 CB MET A 1 11.971 15.000 12.927 1.00 10.00 A C ATOM 2 CG MET A 1 12.074 15.930 14.126 1.00 10.00 A C ATOM 3 SD MET A 1 12.820 17.522 13.722 1.00 10.00 A S ATOM 4 CE MET A 1 14.460 17.016 13.210 1.00 10.00 A C ATOM 5 C MET A 1 11.191 12.831 11.962 1.00 10.00 A C ATOM 6 O MET A 1 12.202 12.489 11.349 1.00 10.00 A O ATOM 7 CA MET A 1 11.294 13.663 13.235 1.00 10.00 A C ATOM 8 N MET A 1 12.057 12.926 14.282 1.00 10.00 A N ATOM 9 D1 MET A 1 11.949 13.331 15.067 1.00 10.00 A D ATOM 10 D2 MET A 1 11.756 12.090 14.335 1.00 10.00 A D ATOM 11 D3 MET A 1 12.921 12.918 14.068 1.00 10.00 A D ATOM 12 DA MET A 1 10.401 13.848 13.565 1.00 10.00 A D ATOM 13 DB2 MET A 1 12.870 14.826 12.608 1.00 10.00 A D ATOM 14 DB3 MET A 1 11.461 15.457 12.240 1.00 10.00 A D ATOM 15 DG2 MET A 1 11.184 16.097 14.473 1.00 10.00 A D ATOM 16 DG3 MET A 1 12.621 15.508 14.806 1.00 10.00 A D ATOM 17 DE1 MET A 1 15.002 17.807 13.062 1.00 10.00 A D ATOM 18 DE2 MET A 1 14.854 16.470 13.909 1.00 10.00 A D ATOM 19 DE3 MET A 1 14.391 16.504 12.389 1.00 10.00 A D TER 20 MET A 1 ATOM 23 O HOH S 2 16.970 14.660 13.630 1.00 10.00 A O ATOM 24 D1 HOH S 2 16.521 14.044 13.276 1.00 10.00 A D ATOM 25 D2 HOH S 2 16.766 15.370 13.231 1.00 10.00 A D ATOM 26 O HOH S 3 12.348 17.911 10.504 1.00 10.00 A O ATOM 27 D1 HOH S 3 13.109 18.034 10.836 1.00 10.00 A D ATOM 28 D2 HOH S 3 11.846 17.664 11.131 1.00 10.00 A D ATOM 29 O HOH S 4 16.209 14.723 11.119 1.00 10.00 A O ATOM 30 D1 HOH S 4 16.097 13.893 11.190 1.00 10.00 A D ATOM 31 D2 HOH S 4 15.524 15.028 10.742 1.00 10.00 A D ATOM 32 O HOH S 5 15.249 14.287 16.163 1.00 10.00 A O ATOM 33 D1 HOH S 5 15.149 14.415 15.339 1.00 10.00 A D ATOM 34 D2 HOH S 5 15.157 15.034 16.537 1.00 10.00 A D ATOM 35 O HOH S 6 17.607 13.216 16.419 1.00 10.00 A O ATOM 36 D1 HOH S 6 17.291 12.646 16.949 1.00 10.00 A D ATOM 37 D2 HOH S 6 17.622 13.948 16.831 1.00 10.00 A D ATOM 38 O HOH S 7 13.968 17.831 16.964 1.00 10.00 A O ATOM 39 D1 HOH S 7 14.750 17.530 17.006 1.00 10.00 A D ATOM 40 D2 HOH S 7 13.867 18.338 17.627 1.00 10.00 A D ATOM 41 O HOH S 8 13.431 20.300 13.702 1.00 10.00 A O ATOM 42 D1 HOH S 8 13.991 20.901 13.877 1.00 10.00 A D ATOM 43 D2 HOH S 8 12.704 20.536 14.050 1.00 10.00 A D ATOM 44 O HOH S 9 19.173 15.952 13.349 1.00 10.00 A O ATOM 45 D1 HOH S 9 18.824 16.704 13.212 1.00 10.00 A D ATOM 46 D2 HOH S 9 18.730 15.586 13.961 1.00 10.00 A D ATOM 59 O HOH S 14 14.246 13.051 9.708 1.00 10.00 A O ATOM 60 D1 HOH S 14 15.046 12.794 9.718 1.00 10.00 A D ATOM 61 D2 HOH S 14 13.805 12.489 10.150 1.00 10.00 A D ATOM 62 O HOH S 15 14.459 12.209 12.550 1.00 10.00 A O ATOM 63 D1 HOH S 15 15.250 12.283 12.277 1.00 10.00 A D ATOM 64 D2 HOH S 15 14.028 12.850 12.221 1.00 10.00 A D ATOM 65 O HOH S 16 13.958 12.275 16.789 1.00 10.00 A O ATOM 66 D1 HOH S 16 14.738 12.322 17.099 1.00 10.00 A D ATOM 67 D2 HOH S 16 13.977 12.633 16.030 1.00 10.00 A D ATOM 68 O HOH S 17 13.943 10.162 15.404 1.00 10.00 A O ATOM 69 D1 HOH S 17 14.704 10.494 15.279 1.00 10.00 A D ATOM 70 D2 HOH S 17 13.509 10.274 14.694 1.00 10.00 A D ATOM 71 O HOH S 18 13.082 14.321 17.799 1.00 10.00 A O ATOM 72 D1 HOH S 18 13.768 14.252 18.278 1.00 10.00 A D ATOM 73 D2 HOH S 18 12.594 13.660 17.976 1.00 10.00 A D ATOM 74 O HOH S 19 16.233 12.348 14.233 1.00 10.00 A O ATOM 75 D1 HOH S 19 16.721 12.270 14.913 1.00 10.00 A D ATOM 76 D2 HOH S 19 15.438 12.353 14.504 1.00 10.00 A D TER 66 HOH S 19 END """ def exercise(d_min = 1.0, resolution_factor=0.2): # Fit HOH or DOD into density map # # answer model and map pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_answer) pdb_inp.write_pdb_file(file_name = "answer.pdb") xrs_answer = pdb_inp.xray_structure_simple() xrs_answer.switch_to_neutron_scattering_dictionary() f_calc_answer = xrs_answer.structure_factors(d_min = d_min).f_calc() fft_map = f_calc_answer.fft_map(resolution_factor=resolution_factor) fft_map.apply_volume_scaling() target_map = fft_map.real_map_unpadded() mtz_dataset = f_calc_answer.as_mtz_dataset(column_root_label = "FCmap") mtz_object = mtz_dataset.mtz_object() mtz_object.write(file_name = "answer.mtz") # poor model (DOD randomly shifted) mon_lib_srv = monomer_library.server.server() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = monomer_library.server.ener_lib(), raw_records = flex.std_string(pdb_poor.splitlines()), strict_conflict_handling = True, force_symmetry = True, log = None) pdb_hierarchy_poor = processed_pdb_file.all_chain_proxies.pdb_hierarchy xrs_poor = processed_pdb_file.xray_structure() xrs_poor.switch_to_neutron_scattering_dictionary() pdb_hierarchy_poor.write_pdb_file(file_name = "poor.pdb") # real-space refine DOD to fit target_map best mmtbx.refinement.real_space.fit_water.run( pdb_hierarchy = pdb_hierarchy_poor, target_map = target_map, unit_cell = xrs_poor.unit_cell(), real_space_gradients_delta = d_min*resolution_factor, log = sys.stdout) # best refined model pdb_hierarchy_poor.write_pdb_file(file_name = "refined.pdb") xrs_refined = pdb_hierarchy_poor.extract_xray_structure( crystal_symmetry = xrs_poor.crystal_symmetry()) xrs_refined.switch_to_neutron_scattering_dictionary() # check results def r_factor(x,y): x = abs(x).data() y = abs(y).data() n = flex.sum(flex.abs(x-y)) d = flex.sum(flex.abs(x+y))/2 return n/d fc_poor = f_calc_answer.structure_factors_from_scatterers( xray_structure = xrs_poor).f_calc() fc_refined = f_calc_answer.structure_factors_from_scatterers( xray_structure = xrs_refined).f_calc() assert r_factor(f_calc_answer, fc_poor) > 0.45 assert r_factor(f_calc_answer, fc_refined) < 0.08 if(__name__ == "__main__"): t0 = time.time() exercise() print("Time: %6.4f"%(time.time()-t0))