def exercise_00(reflections_per_bin=150): """ tncs_epsfac calculation with radius refinement """ pdb_file = libtbx.env.find_in_repositories( relative_path="mmtbx/regression/tncs/model_1.pdb", test=os.path.isfile) pdb_inp = iotbx.pdb.input(file_name=pdb_file) xray_structure = pdb_inp.xray_structure_simple() for b in [0, 50, 100, 200, 400, 800]: xray_structure = xray_structure.set_b_iso(value=b) print "B: %5.1f"%b for d_min in [2,3,4,6,8]: f_obs = abs(xray_structure.structure_factors(d_min=d_min).f_calc()) f_obs = f_obs.set_observation_type_xray_amplitude() result = tncs.compute_eps_factor( f_obs = f_obs, pdb_hierarchy = pdb_inp.construct_hierarchy(), reflections_per_bin = reflections_per_bin) M2 = f_obs.second_moments_centric_acentric( reflections_per_bin = reflections_per_bin) M2_corr = f_obs.second_moments_centric_acentric( reflections_per_bin = reflections_per_bin, eps_fac = result.epsfac) fmt=" d_min: %5.1f R: refined %4.1f estimate %4.1f 2nd Mom.:" print fmt%(d_min, result.ncs_pairs[0].radius, result.ncs_pairs[0].radius_estimate), "%s %4.2f"%M2[0], "%s %4.2f"%M2_corr[0] # this shows summary for the result corresponding to last trial B and d_min result.show_summary()
def exercise_00(reflections_per_bin=150): """ tncs_epsfac calculation with radius refinement """ pdb_file = libtbx.env.find_in_repositories( relative_path="mmtbx/regression/tncs/model_1.pdb", test=os.path.isfile) pdb_inp = iotbx.pdb.input(file_name=pdb_file) xray_structure = pdb_inp.xray_structure_simple() for b in [0, 50, 100, 200, 400, 800]: xray_structure = xray_structure.set_b_iso(value=b) print("B: %5.1f" % b) for d_min in [2, 3, 4, 6, 8]: f_obs = abs(xray_structure.structure_factors(d_min=d_min).f_calc()) f_obs = f_obs.set_observation_type_xray_amplitude() result = tncs.compute_eps_factor( f_obs=f_obs, pdb_hierarchy=pdb_inp.construct_hierarchy(), reflections_per_bin=reflections_per_bin) M2 = f_obs.second_moments_centric_acentric( reflections_per_bin=reflections_per_bin) M2_corr = f_obs.second_moments_centric_acentric( reflections_per_bin=reflections_per_bin, eps_fac=result.epsfac) fmt = " d_min: %5.1f R: refined %4.1f estimate %4.1f 2nd Mom.:" print( fmt % (d_min, result.ncs_pairs[0].radius, result.ncs_pairs[0].radius_estimate), "%s %4.2f" % M2[0], "%s %4.2f" % M2_corr[0]) # this shows summary for the result corresponding to last trial B and d_min result.show_summary()
def exercise_01(reflections_per_bin=150): """ tncs_epsfac calculation with radius refinement """ pdb_file = libtbx.env.find_in_repositories( relative_path="mmtbx/regression/tncs/model_4.pdb", test=os.path.isfile) pdb_inp = iotbx.pdb.input(file_name=pdb_file) xray_structure = pdb_inp.xray_structure_simple() xray_structure = xray_structure.set_b_iso(value=10) f_obs = abs(xray_structure.structure_factors(d_min=2).f_calc()) f_obs = f_obs.set_observation_type_xray_amplitude() result = tncs.compute_eps_factor( f_obs=f_obs, pdb_hierarchy=pdb_inp.construct_hierarchy(), reflections_per_bin=reflections_per_bin) result.show_summary() M2 = f_obs.second_moments_centric_acentric( reflections_per_bin=reflections_per_bin) M2_corr = f_obs.second_moments_centric_acentric( reflections_per_bin=reflections_per_bin, eps_fac=result.epsfac) print("%s %4.2f" % M2[0], "%s %4.2f" % M2_corr[0])
def exercise_01(reflections_per_bin=150): """ tncs_epsfac calculation with radius refinement """ pdb_file = libtbx.env.find_in_repositories( relative_path="mmtbx/regression/tncs/model_4.pdb", test=os.path.isfile) pdb_inp = iotbx.pdb.input(file_name=pdb_file) xray_structure = pdb_inp.xray_structure_simple() xray_structure = xray_structure.set_b_iso(value=10) f_obs = abs(xray_structure.structure_factors(d_min=2).f_calc()) f_obs = f_obs.set_observation_type_xray_amplitude() result = tncs.compute_eps_factor( f_obs = f_obs, pdb_hierarchy = pdb_inp.construct_hierarchy(), reflections_per_bin = reflections_per_bin) result.show_summary() M2 = f_obs.second_moments_centric_acentric( reflections_per_bin = reflections_per_bin) M2_corr = f_obs.second_moments_centric_acentric( reflections_per_bin = reflections_per_bin, eps_fac = result.epsfac) print "%s %4.2f"%M2[0], "%s %4.2f"%M2_corr[0]