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]
