from __future__ import absolute_import, division, print_function from libtbx import easy_run from mmtbx.command_line import cif_as_mtz from iotbx import mtz from iotbx import file_reader from libtbx.test_utils import approx_equal def exercise1(): cif_in = """\ data_r2etdsf # _cell.entry_id 2etd _cell.length_a 80.4540 _cell.length_b 85.2590 _cell.length_c 53.3970 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 90.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength 1 1.0163 2 0.9797 3 0.9796 #_entry.id 2etd # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 2etd _symmetry.space_group_name_H-M 'C 2 2 2' # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.F_meas_au _refln.F_meas_sigma_au _refln.F_calc _refln.phase_calc 1 1 1 0 2 8 o 149.0 3.1 558.1 0.0 1 1 1 0 2 9 o 217.9 4.3 119.3 180.0 1 1 1 0 2 10 o 33.3 5.3 340.6 180.0 1 1 1 0 2 11 o 389.0 10.0 692.8 0.0 1 1 1 0 2 12 o 143.5 3.7 54.5 180.0 1 1 1 0 2 13 f 801.4 36.0 1185.6 0.0 1 1 1 0 2 14 o 351.5 11.8 403.6 360.0 1 1 1 0 2 15 o 439.4 17.2 644.6 180.0 1 1 1 0 2 16 o 39.5 6.8 161.6 180.0 #END data_r2etdAsf # _cell.entry_id 2etd _cell.length_a 80.454 _cell.length_b 85.259 _cell.length_c 53.397 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ; unmerged original index intensities of data set used for refinement and phasing. ; # _entry.id 2etd # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 1 1 1 0 2 -8 o 1544.6 130.4 1 1 1 0 2 9 o 3450.1 264.9 1 1 1 0 -2 9 o 3243.5 268.5 1 1 1 0 -2 -9 o 3475.4 265.0 1 1 1 0 2 -9 o 3420.1 260.3 1 1 1 0 2 10 o 58.8 31.8 1 1 1 0 -2 -10 o 131.7 50.7 1 1 1 0 2 -10 o 97.9 48.7 1 1 1 0 -2 11 o 9808.3 953.5 1 1 1 0 -2 -11 o 11486.1 970.3 1 1 1 0 2 -11 o 11278.1 967.8 1 1 1 0 2 12 o 1368.9 150.7 1 1 1 0 -2 12 o 1620.9 148.7 1 1 1 0 -2 -12 o 1293.5 147.6 1 1 1 0 2 -12 o 1619.5 155.7 1 1 1 0 -2 13 o 47438.3 4104.1 1 1 1 0 2 14 o 8577.5 1188.0 1 1 1 0 -2 14 o 7996.7 1179.9 1 1 1 0 -2 -14 o 9333.7 1178.1 1 1 1 0 2 -14 o 9642.3 1197.6 1 1 1 0 2 15 o 13577.7 1852.4 1 1 1 0 -2 15 o 14100.9 1852.8 1 1 1 0 -2 -15 o 14184.2 1871.6 1 1 1 0 2 16 o 135.6 76.3 1 1 1 0 -2 16 o 117.0 60.4 #END data_r2etdBsf # _cell.entry_id 2etd _cell.length_a 80.419 _cell.length_b 85.227 _cell.length_c 53.389 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' unmerged original index intensities of data set used for phasing.' # _entry.id 2etd # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 1 2 1 0 2 8 o 1095.4 110.5 1 2 1 0 -2 8 o 1105.1 117.9 1 2 1 0 -2 -8 o 1055.4 108.6 1 2 1 0 2 -8 o 1105.1 118.0 1 2 1 0 2 9 o 3795.1 366.5 1 2 1 0 -2 9 o 3925.3 371.7 1 2 1 0 -2 -9 o 3726.2 366.9 1 2 1 0 2 -9 o 3899.3 371.8 1 2 1 0 2 10 o 27.0 40.7 1 2 1 0 -2 10 o 80.7 34.8 1 2 1 0 -2 -10 o 18.3 40.3 1 2 1 0 2 -10 o 16.5 45.4 1 2 1 0 2 11 o 10830.4 977.6 1 2 1 0 -2 11 o 9647.1 972.1 1 2 1 0 -2 -11 o 10854.6 983.4 1 2 1 0 2 -11 o 10369.4 976.0 1 2 1 0 2 12 o 1143.7 131.7 1 2 1 0 -2 12 o 1378.0 140.1 1 2 1 0 -2 -12 o 1090.9 134.2 1 2 1 0 2 -12 o 1290.6 135.6 1 2 1 0 -2 13 o 44492.5 4083.0 1 2 1 0 2 -13 o 44931.1 4102.4 1 2 1 0 2 14 o 6646.0 952.7 1 2 1 0 -2 14 o 6516.6 949.1 1 2 1 0 -2 -14 o 7589.5 952.0 1 2 1 0 2 -14 o 7559.7 954.2 1 2 1 0 2 16 o 256.6 68.6 1 2 1 0 -2 16 o 137.1 67.8 1 2 1 0 -2 -16 o 307.6 69.9 1 2 1 0 2 -16 o 265.4 71.5 """ with open("r2etd-sf.cif", "w") as f: f.write(cif_in) args = ["phenix.cif_as_mtz", "r2etd-sf.cif", "--merge"] rc = easy_run.fully_buffered(" ".join(args)).raise_if_errors().return_code assert (rc == 0) hkl_in = file_reader.any_file("r2etd-sf.mtz") l_w = [] for array in hkl_in.file_server.miller_arrays : l_w.append((array.info().label_string(), "%.4f" % array.info().wavelength)) assert (sorted(l_w) == sorted([ ('FOBS,SIGFOBS', '1.0163'), ('FC,PHIFC', '1.0163'), ('R-free-flags', '1.0163'), ('I(+),SIGI(+),I(-),SIGI(-)', '1.0163'), ('I2(+),SIGI2(+),I2(-),SIGI2(-)', '0.9797') ]) ) r1vjzsf_cif_snip = """ data_r1vjzsf # loop_ _audit.revision_id _audit.creation_date _audit.update_record 1 2004-04-13 'initial processing' 1_1 2009-01-27 'correct token name _refln.pdbx_HLA (_HLB, _HLC, _HLD)' 1_2 2013-12-04 'Format standardization' # _cell.entry_id 1vjz _cell.length_a 64.6840 _cell.length_b 64.6840 _cell.length_c 202.1890 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 90.0000 # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength 1 0.98050 2 0.964063 3 0.979292 # _entry.id 1vjz # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 1vjz _symmetry.space_group_name_H-M 'P 43 21 2' # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.F_meas_au _refln.F_meas_sigma_au _refln.F_calc _refln.phase_calc 1 1 1 0 0 4 x ? ? ? ? 1 1 1 0 0 8 x ? ? 7109.5 180.0 1 1 1 0 0 12 x ? ? 8288.9 0.0 1 1 1 0 0 16 x ? ? 61.6 180.0 1 1 1 0 0 88 x ? ? 152.2 180.0 1 1 1 0 0 92 x ? ? 283.3 180.0 1 1 1 0 0 96 x ? ? 4.0 0.0 1 1 1 1 0 4 x ? ? ? ? 1 1 1 1 0 5 x ? ? ? ? 1 1 1 1 0 6 o 2.9 2.2 2024.1 180.0 1 1 1 1 0 20 x ? ? 156.2 90.0 1 1 1 1 0 21 x ? ? 55.4 225.0 1 1 1 1 0 22 x ? ? 372.1 0.0 1 1 1 1 0 23 x ? ? 787.1 315.0 1 1 1 1 0 24 x ? ? 1019.9 90.0 1 1 1 29 1 32 o 65.1 31.3 51.5 162.3 1 1 1 29 1 33 o 114.8 41.1 158.8 333.1 1 1 1 29 1 34 o 56.3 26.4 91.5 288.3 1 1 1 29 1 35 o 65.4 30.2 25.1 310.6 1 1 1 29 1 36 o 153.4 30.3 186.2 324.9 1 1 1 29 1 37 o 93.5 34.8 98.6 95.9 1 1 1 29 1 38 o 169.8 28.2 162.2 118.8 1 1 1 29 2 0 o 34.4 24.5 34.0 0.0 1 1 1 31 3 0 x ? ? 60.1 180.0 1 1 1 31 3 1 x ? ? 67.5 280.1 1 1 1 31 5 4 x ? ? 34.2 340.2 1 1 1 31 5 5 x ? ? 87.2 143.7 1 1 1 31 5 6 x ? ? 98.8 296.4 1 1 1 31 5 7 x ? ? 82.1 258.8 1 1 1 31 5 8 x ? ? 26.0 52.6 #END data_r1vjzAsf # _cell.entry_id 1vjz _cell.length_a 64.6840 _cell.length_b 64.6840 _cell.length_c 202.1890 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 90.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' unmerged original index intensities of refinement data set from crystal 9787' # _entry.id 1vjz # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 1 1 1 -1 -1 10 o 951.9 69.6 1 1 1 -1 -1 11 o 9456.0 609.5 1 1 1 1 1 -11 o 9620.4 605.4 1 1 1 -1 -1 12 o 16133.9 1012.7 1 1 1 1 1 -12 o 15721.5 1009.6 1 1 1 1 1 -13 o 1927.0 136.7 1 1 1 1 1 -14 o 3807.9 256.6 1 1 1 1 1 -15 o 15116.1 974.6 1 1 1 1 1 -16 o 234.3 31.4 1 1 1 29 -10 17 o -252.6 243.5 1 1 1 29 -10 18 o 156.6 249.9 1 1 1 29 -10 19 o 15.8 240.5 1 1 1 29 -10 20 o -44.9 252.3 1 1 1 -29 10 -21 o 237.6 205.8 1 1 1 29 -10 21 o 355.8 255.2 1 1 1 -29 10 -22 o 39.6 184.6 1 1 1 29 -10 22 o -420.4 253.3 1 1 1 -29 10 -23 o 574.3 226.0 1 1 1 29 -10 23 o 147.9 293.5 1 1 1 30 -6 21 o -767.8 264.6 1 1 1 30 -6 22 o 371.8 262.9 #END data_r1vjzBsf # _cell.entry_id 1vjz _cell.length_a 64.299 _cell.length_b 64.299 _cell.length_c 201.930 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 90.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ; unmerged original index intensities of data set from crystal 9774 for phasing ; # _entry.id 1vjz # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 2 2 1 0 0 -8 o 1242.5 76.9 2 2 1 0 0 16 o 16497.6 696.8 2 2 1 0 0 -16 o 16886.5 627.7 2 2 1 0 0 20 o 1152.8 84.5 2 2 1 0 0 -20 o 1245.8 91.2 2 2 1 0 0 24 o 56057.3 2118.1 2 2 1 0 0 24 o 59770.5 2186.0 2 2 1 -6 -25 3 o 22.2 92.9 2 2 1 -6 25 4 o 277.8 206.5 2 2 1 -6 -25 -4 o 68.3 87.2 2 2 1 -6 25 -4 o 160.7 147.9 2 2 1 -6 -25 4 o 91.5 93.8 2 2 1 -6 25 5 o -91.5 130.8 2 2 1 -6 -25 -5 o 97.6 104.4 2 2 1 -6 25 -5 o 130.0 106.8 2 2 1 -6 -25 5 o -9.6 109.3 2 2 1 6 25 5 o 67.3 80.6 2 2 1 -6 25 -6 o -41.7 118.2 2 2 1 -6 -25 6 o 30.7 107.1 #END data_r1vjzCsf # _cell.entry_id 1vjz _cell.length_a 64.635 _cell.length_b 64.635 _cell.length_c 202.270 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 90.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ; unmerged original index intensities of data set from crystal 9774 for phasing ; # _entry.id 1vjz # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 2 3 1 0 0 8 o 933.7 60.3 2 3 1 0 0 -8 o 984.1 57.7 2 3 1 0 0 16 o 15152.9 586.0 2 3 1 0 0 -16 o 14897.3 566.8 2 3 1 0 0 20 o 772.2 57.1 2 3 1 0 0 -20 o 816.3 77.3 2 3 1 5 -25 -8 o 57.2 193.8 2 3 1 5 -25 9 o -43.3 123.1 2 3 1 5 25 -9 o 59.0 148.2 2 3 1 -5 25 -9 o 46.7 207.2 2 3 1 5 -25 -9 o 181.2 215.8 2 3 1 6 25 4 o 215.7 297.9 2 3 1 6 25 -5 o 17.4 108.4 2 3 1 -6 25 -5 o 24.5 124.0 2 3 1 6 25 -6 o 46.3 101.5 2 3 1 -6 25 -6 o 2189.4 287.3 2 3 1 6 25 -7 o 71.2 113.9 2 3 1 -6 25 -7 o -34.1 124.7 2 3 1 -6 25 -8 o 240.5 148.9 #END data_r1vjzDsf # _cell.entry_id 1vjz _cell.length_a 64.299 _cell.length_b 64.299 _cell.length_c 201.930 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 90.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' phases from crystal 9774' # _entry.id 1vjz # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.pdbx_HL_A_iso _refln.pdbx_HL_B_iso _refln.pdbx_HL_C_iso _refln.pdbx_HL_D_iso 2 2 1 0 0 4 o ? ? ? ? 2 2 1 0 0 8 o -28.66 0.00 0.00 0.00 2 2 1 0 0 12 o ? ? ? ? 2 2 1 0 0 16 o -39.51 0.00 0.00 0.00 2 2 1 0 0 20 o -59.59 0.00 0.00 0.00 2 2 1 0 0 24 o 0.91 0.00 0.00 0.00 2 2 1 0 0 28 o -19.74 0.00 0.00 0.00 2 2 1 0 0 32 o -56.97 0.00 0.00 0.00 2 2 1 25 4 15 o 0.02 0.27 0.00 0.01 2 2 1 25 4 16 o ? ? ? ? 2 2 1 25 5 0 o 0.13 0.00 0.00 0.00 2 2 1 25 5 1 o -0.20 0.12 0.00 0.00 2 2 1 25 5 13 o ? ? ? ? 2 2 1 25 6 0 o -0.24 0.00 0.00 0.00 2 2 1 25 6 1 o -0.42 0.45 0.01 0.00 2 2 1 25 6 2 o 0.06 -0.49 0.00 0.00 2 2 1 25 6 3 o 0.48 0.32 0.00 -0.01 2 2 1 25 6 4 o -0.36 -0.21 0.00 0.00 2 2 1 25 6 5 o -0.06 -0.05 0.00 0.00 2 2 1 25 6 6 o -0.51 -0.49 0.00 0.00 2 2 1 25 6 7 o ? ? ? ? 2 2 1 25 6 8 o ? ? ? ? #END OF REFLECTIONS """ def exercise2(): """ Check individual unit cell dimensions and wavelengths of cif datasets are retained when reading an mtz file originating from a cif file """ with open("r1vjzsf_snip.cif", "w") as f: f.write(r1vjzsf_cif_snip) args = ["phenix.cif_as_mtz", "r1vjzsf_snip.cif", "--merge"] rc = easy_run.fully_buffered(" ".join(args)).raise_if_errors().return_code assert (rc == 0) hkl_in = file_reader.any_file("r1vjzsf_snip.mtz") l_w = [] for array in hkl_in.file_server.miller_arrays: uc = array.unit_cell().parameters() l_w.append((array.info().label_string(), "%.5f"%array.info().wavelength, "%.4f"%uc[0], "%.4f"%uc[1], "%.4f"%uc[2], "%.3f"%uc[3], "%.3f"%uc[4], "%.3f"%uc[5])) assert (sorted(l_w) == sorted([ ('R-free-flags', '0.98050', '64.6840', '64.6840', '202.1890', '90.000', '90.000', '90.000'), ('FOBS,SIGFOBS', '0.98050', '64.6840', '64.6840', '202.1890', '90.000', '90.000', '90.000'), ('FC,PHIFC', '0.98050', '64.6840', '64.6840', '202.1890', '90.000', '90.000', '90.000'), ('I(+),SIGI(+),I(-),SIGI(-)', '0.98050', '64.6840', '64.6840', '202.1890', '90.000', '90.000', '90.000'), ('I2(+),SIGI2(+),I2(-),SIGI2(-)', '0.96406', '64.2990', '64.2990', '201.9300', '90.000', '90.000', '90.000'), ('I3(+),SIGI3(+),I3(-),SIGI3(-)', '0.97929', '64.6350', '64.6350', '202.2700', '90.000', '90.000', '90.000'), ('R-free-flags2', '0.96406', '64.2990', '64.2990', '201.9300', '90.000', '90.000', '90.000'), ('HLA,HLB,HLC,HLD', '0.96406', '64.2990', '64.2990', '201.9300', '90.000', '90.000', '90.000') ]) ) def exercise3(): """ Check individual unit cell dimensions and wavelengths of cif datasets are retained in mtz crystals within the same mtz file """ with open("r1vjzsf_snip.cif", "w") as f: f.write(r1vjzsf_cif_snip) args = ["phenix.cif_as_mtz", "r1vjzsf_snip.cif", "--merge"] rc = easy_run.fully_buffered(" ".join(args)).raise_if_errors().return_code assert (rc == 0) m = mtz.object(file_name="r1vjzsf_snip.mtz") assert (len(m.crystals()) == 5) eps = 1.e-5 assert approx_equal(m.crystals()[1].datasets()[0].wavelength(), 0.98049998, eps) assert approx_equal(m.crystals()[2].datasets()[0].wavelength(), 0.96406001, eps) assert approx_equal(m.crystals()[3].datasets()[0].wavelength(), 0.97929000, eps) assert approx_equal(m.crystals()[4].datasets()[0].wavelength(), 0.96406000, eps) uc = m.crystals()[1].unit_cell_parameters() fuc = "%.4f"%uc[0], "%.4f"%uc[1], "%.4f"%uc[2], "%.3f"%uc[3], "%.3f"%uc[4], "%.3f"%uc[5] assert (('64.6840', '64.6840', '202.1890', '90.000', '90.000', '90.000') == fuc) uc = m.crystals()[2].unit_cell_parameters() fuc = "%.4f"%uc[0], "%.4f"%uc[1], "%.4f"%uc[2], "%.3f"%uc[3], "%.3f"%uc[4], "%.3f"%uc[5] assert (('64.2990', '64.2990', '201.9300', '90.000', '90.000', '90.000') == fuc) uc = m.crystals()[3].unit_cell_parameters() fuc = "%.4f"%uc[0], "%.4f"%uc[1], "%.4f"%uc[2], "%.3f"%uc[3], "%.3f"%uc[4], "%.3f"%uc[5] assert (('64.6350', '64.6350', '202.2700', '90.000', '90.000', '90.000') == fuc) uc = m.crystals()[4].unit_cell_parameters() fuc = "%.4f"%uc[0], "%.4f"%uc[1], "%.4f"%uc[2], "%.3f"%uc[3], "%.3f"%uc[4], "%.3f"%uc[5] assert (('64.2990', '64.2990', '201.9300', '90.000', '90.000', '90.000') == fuc) if (__name__ == "__main__"): exercise1() exercise2() exercise3() print("OK")