from __future__ import division from libtbx import easy_run def exercise () : from mmtbx.command_line import cif_as_mtz from iotbx import file_reader 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 """ open("r2etd-sf.cif", "w").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 (l_w == [ ('FC,PHIFC', '1.0163'), ('FOBS,SIGFOBS', '1.0163'), ('R-free-flags', '1.0163'), ('I(+),SIGI(+),I(-),SIGI(-)', '1.0163'), ('I2(+),SIGI2(+),I2(-),SIGI2(-)', '0.9797') ]) if (__name__ == "__main__") : exercise() print "OK"