def exercise_1():
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1yjp_h.pdb",
test=os.path.isfile)
mtz_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/1yjp.mtz",
test=os.path.isfile)
if (None in [pdb_file, mtz_file]) :
print "phenix_regression not found, skipping test"
return False
pdb_in = file_reader.any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy.atoms().reset_i_seq()
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = file_reader.any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0]
r_free = mtz_in.file_server.miller_arrays[1]
r_free = r_free.customized_copy(data=(r_free.data()==1))
fmodel = mmtbx.utils.fmodel_simple(
f_obs=f_obs,
r_free_flags=r_free,
xray_structures=[xrs],
scattering_table="n_gaussian")
map_stats = real_space_correlation.map_statistics_for_fragment(
fragment=hierarchy,
fmodel=fmodel)
assert approx_equal(map_stats.cc, 0.960, eps=0.01)
edm = fmodel.electron_density_map()
map1_coeffs = edm.map_coefficients("2mFo-DFc")
map1 = map1_coeffs.fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map()
map2_coeffs = edm.map_coefficients("Fmodel")
map2 = map2_coeffs.fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map()
xray_structure = fmodel.xray_structure
map_stats2 = real_space_correlation.map_statistics_for_atom_selection(
atom_selection=flex.bool(xrs.sites_cart().size(), True),
map1=map1,
map2=map2,
xray_structure=xrs)
assert approx_equal(map_stats2.cc, map_stats.cc, 0.01)
# XXX other code outside cctbx depends on the current API - do not simply
# change the test if this breaks!
results = real_space_correlation.simple(
fmodel=fmodel,
pdb_hierarchy=hierarchy,
log=null_out())
assert isinstance(results, list)
assert isinstance(results[0], group_args)
assert (results[0].n_atoms == 1)
assert (results[0].id_str == " A GLY 1 N ")
return True
def exercise_1():
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1yjp_h.pdb", test=os.path.isfile)
mtz_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/1yjp.mtz",
test=os.path.isfile)
if (None in [pdb_file, mtz_file]):
print "phenix_regression not found, skipping test"
return False
pdb_in = file_reader.any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy.atoms().reset_i_seq()
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = file_reader.any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0]
r_free = mtz_in.file_server.miller_arrays[1]
r_free = r_free.customized_copy(data=(r_free.data() == 1))
fmodel = mmtbx.utils.fmodel_simple(f_obs=f_obs,
r_free_flags=r_free,
xray_structures=[xrs],
scattering_table="n_gaussian")
map_stats = real_space_correlation.map_statistics_for_fragment(
fragment=hierarchy, fmodel=fmodel)
assert approx_equal(map_stats.cc, 0.960, eps=0.01)
edm = fmodel.electron_density_map()
map1_coeffs = edm.map_coefficients("2mFo-DFc")
map1 = map1_coeffs.fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map()
map2_coeffs = edm.map_coefficients("Fmodel")
map2 = map2_coeffs.fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map()
xray_structure = fmodel.xray_structure
map_stats2 = real_space_correlation.map_statistics_for_atom_selection(
atom_selection=flex.bool(xrs.sites_cart().size(), True),
map1=map1,
map2=map2,
xray_structure=xrs)
assert approx_equal(map_stats2.cc, map_stats.cc, 0.01)
# XXX other code outside cctbx depends on the current API - do not simply
# change the test if this breaks!
overall_cc, results = real_space_correlation.simple(
fmodel=fmodel, pdb_hierarchy=hierarchy, log=null_out())
assert isinstance(overall_cc, float)
assert isinstance(results, list)
assert isinstance(results[0], group_args)
assert (results[0].n_atoms == 1)
assert (results[0].id_str == " A GLY 1 N ")
return True
def one_water_correlation(model, fmodels, water):
import mmtbx.solvent.ordered_solvent as ordered_solvent
from mmtbx import real_space_correlation
params = ordered_solvent.master_params().extract()
par = params.secondary_map_and_map_cc_filter
rcparams = real_space_correlation.master_params().extract()
rcparams.detail = "residue"
if fmodels.fmodel_n is not None:
fmodel = fmodels.fmodel_neutron()
else:
fmodel = fmodels.fmodel_xray()
title = "xray"
if fmodel.xray_structure.guess_scattering_type_neutron():
title = "neutron"
scatterers = model.get_xray_structure().scatterers()
assert scatterers is fmodel.xray_structure.scatterers()
results = real_space_correlation.map_statistics_for_atom_selection(
atom_selection=water,
fmodel=fmodel,
map1_type="Fo",
map2_type="Fmodel")
return results.cc
def one_water_correlation(model, fmodels, water):
import mmtbx.solvent.ordered_solvent as ordered_solvent
from mmtbx import real_space_correlation
params = ordered_solvent.master_params().extract()
par = params.secondary_map_and_map_cc_filter
rcparams = real_space_correlation.master_params().extract()
rcparams.detail = "residue"
if fmodels.fmodel_n is not None:
fmodel = fmodels.fmodel_neutron()
else:
fmodel = fmodels.fmodel_xray()
title = "xray"
if fmodel.xray_structure.guess_scattering_type_neutron():
title="neutron"
scatterers = model.xray_structure.scatterers()
assert scatterers is fmodel.xray_structure.scatterers()
results = real_space_correlation.map_statistics_for_atom_selection(
atom_selection = water,
fmodel = fmodel,
map1_type="Fo",
map2_type="Fmodel"
)
return results.cc
def exercise_2():
pdb_str = """\
CRYST1 12.000 8.000 12.000 90.02 89.96 90.05 P 1 1
ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N
ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C
ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C
ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O
ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C
ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C
ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O
ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N
ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N
ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C
ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C
ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O
ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C
ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C
ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C
ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C
ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C
ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C
ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C
ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O
ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O
TER
ATOM 1 N ASN B 6 1.414 5.113 6.019 1.00 12.99 N
ATOM 2 CA ASN B 6 2.720 4.776 5.445 1.00 13.30 C
ATOM 3 C ASN B 6 3.763 5.209 6.438 1.00 14.40 C
ATOM 4 O ASN B 6 4.125 6.391 6.507 1.00 14.92 O
ATOM 5 CB ASN B 6 2.922 5.513 4.131 1.00 13.13 C
ATOM 6 CG ASN B 6 1.798 5.250 3.160 1.00 13.77 C
ATOM 7 OD1 ASN B 6 1.629 4.129 2.686 1.00 15.27 O
ATOM 8 ND2 ASN B 6 1.022 6.266 2.875 1.00 11.07 N
ATOM 9 N TYR B 7 4.222 4.248 7.230 1.00 15.70 N
ATOM 10 CA TYR B 7 5.113 4.552 8.370 1.00 16.18 C
ATOM 11 C TYR B 7 6.547 4.754 7.929 1.00 16.91 C
ATOM 12 O TYR B 7 6.964 4.259 6.878 1.00 16.76 O
ATOM 13 CB TYR B 7 5.042 3.449 9.417 1.00 16.35 C
ATOM 14 CG TYR B 7 3.659 3.296 9.977 1.00 15.45 C
ATOM 15 CD1 TYR B 7 2.756 2.398 9.402 1.00 16.68 C
ATOM 16 CD2 TYR B 7 3.224 4.098 11.023 1.00 15.80 C
ATOM 17 CE1 TYR B 7 1.476 2.267 9.896 1.00 14.46 C
ATOM 18 CE2 TYR B 7 1.929 3.975 11.545 1.00 15.33 C
ATOM 19 CZ TYR B 7 1.063 3.065 10.959 1.00 16.09 C
ATOM 20 OH TYR B 7 -0.207 2.910 11.443 1.00 15.39 O
ATOM 21 OXT TYR B 7 7.316 5.408 8.654 1.00 18.49 O
END
"""
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
xrs = pdb_in.input.xray_structure_simple()
fc = abs(xrs.structure_factors(d_min=1.5).f_calc())
fc = fc.set_observation_type_xray_amplitude()
sigf = flex.double(fc.size(), 0.1) + (fc.data() * 0.03)
fc = fc.customized_copy(sigmas=sigf)
# and now add twinning
fc_twin = fc.twin_data(twin_law='-l,-k,-h', alpha=0.4)
flags = fc_twin.generate_r_free_flags(use_lattice_symmetry=True)
fmodel = mmtbx.utils.fmodel_simple(f_obs=fc_twin,
r_free_flags=flags,
xray_structures=[xrs],
scattering_table="n_gaussian")
assert (fmodel.twin_law is not None)
map_stats = real_space_correlation.extract_map_stats_for_single_atoms(
xray_structure=xrs, pdb_atoms=pdb_in.hierarchy.atoms(), fmodel=fmodel)
sel_cache = pdb_in.hierarchy.atom_selection_cache()
sel = sel_cache.selection("chain B")
map_stats_2 = real_space_correlation.extract_map_stats_for_single_atoms(
xray_structure=xrs,
pdb_atoms=pdb_in.hierarchy.atoms(),
fmodel=fmodel,
selection=sel)
map_stats_3 = real_space_correlation.map_statistics_for_atom_selection(
atom_selection=sel, fmodel=fmodel)
def exercise_2 () :
pdb_str = """\
CRYST1 12.000 8.000 12.000 90.02 89.96 90.05 P 1 1
ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N
ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C
ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C
ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O
ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C
ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C
ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O
ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N
ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N
ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C
ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C
ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O
ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C
ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C
ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C
ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C
ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C
ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C
ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C
ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O
ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O
TER
ATOM 1 N ASN B 6 1.414 5.113 6.019 1.00 12.99 N
ATOM 2 CA ASN B 6 2.720 4.776 5.445 1.00 13.30 C
ATOM 3 C ASN B 6 3.763 5.209 6.438 1.00 14.40 C
ATOM 4 O ASN B 6 4.125 6.391 6.507 1.00 14.92 O
ATOM 5 CB ASN B 6 2.922 5.513 4.131 1.00 13.13 C
ATOM 6 CG ASN B 6 1.798 5.250 3.160 1.00 13.77 C
ATOM 7 OD1 ASN B 6 1.629 4.129 2.686 1.00 15.27 O
ATOM 8 ND2 ASN B 6 1.022 6.266 2.875 1.00 11.07 N
ATOM 9 N TYR B 7 4.222 4.248 7.230 1.00 15.70 N
ATOM 10 CA TYR B 7 5.113 4.552 8.370 1.00 16.18 C
ATOM 11 C TYR B 7 6.547 4.754 7.929 1.00 16.91 C
ATOM 12 O TYR B 7 6.964 4.259 6.878 1.00 16.76 O
ATOM 13 CB TYR B 7 5.042 3.449 9.417 1.00 16.35 C
ATOM 14 CG TYR B 7 3.659 3.296 9.977 1.00 15.45 C
ATOM 15 CD1 TYR B 7 2.756 2.398 9.402 1.00 16.68 C
ATOM 16 CD2 TYR B 7 3.224 4.098 11.023 1.00 15.80 C
ATOM 17 CE1 TYR B 7 1.476 2.267 9.896 1.00 14.46 C
ATOM 18 CE2 TYR B 7 1.929 3.975 11.545 1.00 15.33 C
ATOM 19 CZ TYR B 7 1.063 3.065 10.959 1.00 16.09 C
ATOM 20 OH TYR B 7 -0.207 2.910 11.443 1.00 15.39 O
ATOM 21 OXT TYR B 7 7.316 5.408 8.654 1.00 18.49 O
END
"""
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
xrs = pdb_in.input.xray_structure_simple()
fc = abs(xrs.structure_factors(d_min=1.5).f_calc())
fc = fc.set_observation_type_xray_amplitude()
sigf = flex.double(fc.size(), 0.1) + (fc.data() * 0.03)
fc = fc.customized_copy(sigmas=sigf)
# and now add twinning
fc_twin = fc.twin_data(twin_law='-l,-k,-h', alpha=0.4)
flags = fc_twin.generate_r_free_flags(use_lattice_symmetry=True)
fmodel = mmtbx.utils.fmodel_simple(
f_obs=fc_twin,
r_free_flags=flags,
xray_structures=[xrs],
scattering_table="n_gaussian")
assert (fmodel.twin_law is not None)
map_stats = real_space_correlation.extract_map_stats_for_single_atoms(
xray_structure=xrs,
pdb_atoms=pdb_in.hierarchy.atoms(),
fmodel=fmodel)
sel_cache = pdb_in.hierarchy.atom_selection_cache()
sel = sel_cache.selection("chain B")
map_stats_2 = real_space_correlation.extract_map_stats_for_single_atoms(
xray_structure=xrs,
pdb_atoms=pdb_in.hierarchy.atoms(),
fmodel=fmodel,
selection=sel)
map_stats_3 = real_space_correlation.map_statistics_for_atom_selection(
atom_selection=sel,
fmodel=fmodel)
