def __init__ (self, pdb_hierarchy, xray_structure, fmodel,
distance_cutoff=4.0, collect_all=True,
molprobity_map_params=None) :
validation.__init__(self)
from mmtbx.real_space_correlation import extract_map_stats_for_single_atoms
from cctbx import adptbx
from scitbx.matrix import col
self.n_bad = 0
self.n_heavy = 0
pdb_atoms = pdb_hierarchy.atoms()
if(len(pdb_atoms)>1):
assert (not pdb_atoms.extract_i_seq().all_eq(0))
unit_cell = xray_structure.unit_cell()
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff = distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_cart = xray_structure.sites_cart()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("resname HOH and name O")
if (molprobity_map_params is not None):
# assume parameters have been validated (symmetry of pdb and map matches)
two_fofc_map = None
fc_map = None
d_min = None
crystal_gridding = None
# read two_fofc_map
if (molprobity_map_params.map_file_name is not None):
f = any_file(molprobity_map_params.map_file_name)
two_fofc_map = f.file_object.map_data()
d_min = molprobity_map_params.d_min
crystal_gridding = maptbx.crystal_gridding(
f.file_object.unit_cell(),
space_group_info=space_group_info(f.file_object.space_group_number),
pre_determined_n_real=f.file_object.unit_cell_grid)
elif (molprobity_map_params.map_coefficients_file_name is not None):
f = any_file(molprobity_map_params.map_coefficients_file_name)
fourier_coefficients = f.file_server.get_miller_array(
molprobity_map_params.map_coefficients_label)
crystal_symmetry = fourier_coefficients.crystal_symmetry()
d_min = fourier_coefficients.d_min()
crystal_gridding = maptbx.crystal_gridding(
crystal_symmetry.unit_cell(), d_min, resolution_factor=0.25,
space_group_info=crystal_symmetry.space_group_info())
two_fofc_map = miller.fft_map(
crystal_gridding=crystal_gridding,
fourier_coefficients=fourier_coefficients).apply_sigma_scaling().\
real_map_unpadded()
# calculate fc_map
assert( (d_min is not None) and (crystal_gridding is not None) )
f_calc = xray_structure.structure_factors(d_min=d_min).f_calc()
fc_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_calc)
fc_map = fc_map.apply_sigma_scaling().real_map_unpadded()
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=None,
selection=water_sel,
fc_map=fc_map,
two_fofc_map=two_fofc_map)
else:
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=fmodel,
selection=water_sel)
waters = []
for i_seq, atom in enumerate(pdb_atoms) :
if (water_sel[i_seq]) :
rt_mx_i_inv = asu_mappings.get_rt_mx(i_seq, 0).inverse()
self.n_total += 1
asu_dict = asu_table[i_seq]
nearest_atom = nearest_contact = None
for j_seq, j_sym_groups in asu_dict.items() :
atom_j = pdb_atoms[j_seq]
site_j = sites_frac[j_seq]
# Filter out hydrogens
if atom_j.element.upper().strip() in ["H", "D"]:
continue
for j_sym_group in j_sym_groups:
rt_mx = rt_mx_i_inv.multiply(asu_mappings.get_rt_mx(j_seq,
j_sym_group[0]))
site_ji = rt_mx * site_j
site_ji_cart = xray_structure.unit_cell().orthogonalize(site_ji)
vec_i = col(atom.xyz)
vec_ji = col(site_ji_cart)
dxyz = abs(vec_i - vec_ji)
if (nearest_contact is None) or (dxyz < nearest_contact) :
nearest_contact = dxyz
nearest_atom = atom_info(pdb_atom=atom_j, symop=rt_mx)
w = water(
pdb_atom=atom,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
occupancy=occupancies[i_seq],
nearest_contact=nearest_contact,
nearest_atom=nearest_atom,
score=map_stats.two_fofc_ccs[i_seq],
fmodel=map_stats.fmodel_values[i_seq],
two_fofc=map_stats.two_fofc_values[i_seq],
fofc=map_stats.fofc_values[i_seq],
anom=map_stats.anom_values[i_seq],
n_hbonds=None) # TODO
if (w.is_bad_water()) :
w.outlier = True
self.n_bad += 1
elif (w.is_heavy_atom()) :
w.outlier = True
self.n_heavy += 1
if (w.outlier) or (collect_all) :
self.results.append(w)
self.n_outliers = len(self.results)
def __init__(self,
pdb_hierarchy,
xray_structure,
fmodel,
distance_cutoff=4.0,
collect_all=True,
molprobity_map_params=None):
validation.__init__(self)
from mmtbx.real_space_correlation import extract_map_stats_for_single_atoms
from cctbx import adptbx
from scitbx.matrix import col
self.n_bad = 0
self.n_heavy = 0
pdb_atoms = pdb_hierarchy.atoms()
if (len(pdb_atoms) > 1):
assert (not pdb_atoms.extract_i_seq().all_eq(0))
unit_cell = xray_structure.unit_cell()
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff=distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("water")
if (molprobity_map_params is not None):
# assume parameters have been validated (symmetry of pdb and map matches)
two_fofc_map = None
fc_map = None
d_min = None
crystal_gridding = None
# read two_fofc_map
if (molprobity_map_params.map_file_name is not None):
f = any_file(molprobity_map_params.map_file_name)
two_fofc_map = f.file_object.map_data()
d_min = molprobity_map_params.d_min
crystal_gridding = maptbx.crystal_gridding(
f.file_object.unit_cell(),
space_group_info=space_group_info(
f.file_object.space_group_number),
pre_determined_n_real=f.file_object.unit_cell_grid)
pdb_atoms = pdb_hierarchy.atoms()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=f.crystal_symmetry())
unit_cell = xray_structure.unit_cell()
# check for origin shift
# ---------------------------------------------------------------------
soin = maptbx.shift_origin_if_needed(
map_data=two_fofc_map,
sites_cart=xray_structure.sites_cart(),
crystal_symmetry=xray_structure.crystal_symmetry())
two_fofc_map = soin.map_data
xray_structure.set_sites_cart(soin.sites_cart)
# ---------------------------------------------------------------------
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff=distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("water")
elif (molprobity_map_params.map_coefficients_file_name
is not None):
f = any_file(molprobity_map_params.map_coefficients_file_name)
fourier_coefficients = f.file_server.get_miller_array(
molprobity_map_params.map_coefficients_label)
crystal_symmetry = fourier_coefficients.crystal_symmetry()
d_min = fourier_coefficients.d_min()
crystal_gridding = maptbx.crystal_gridding(
crystal_symmetry.unit_cell(),
d_min,
resolution_factor=0.25,
space_group_info=crystal_symmetry.space_group_info())
two_fofc_map = miller.fft_map(
crystal_gridding=crystal_gridding,
fourier_coefficients=fourier_coefficients).apply_sigma_scaling().\
real_map_unpadded()
# calculate fc_map
assert ((d_min is not None) and (crystal_gridding is not None))
f_calc = xray_structure.structure_factors(d_min=d_min).f_calc()
fc_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_calc)
fc_map = fc_map.apply_sigma_scaling().real_map_unpadded()
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=None,
selection=water_sel,
fc_map=fc_map,
two_fofc_map=two_fofc_map)
else:
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=fmodel,
selection=water_sel)
waters = []
for i_seq, atom in enumerate(pdb_atoms):
if (water_sel[i_seq]):
rt_mx_i_inv = asu_mappings.get_rt_mx(i_seq, 0).inverse()
self.n_total += 1
asu_dict = asu_table[i_seq]
nearest_atom = nearest_contact = None
for j_seq, j_sym_groups in asu_dict.items():
atom_j = pdb_atoms[j_seq]
site_j = sites_frac[j_seq]
# Filter out hydrogens
if atom_j.element.upper().strip() in ["H", "D"]:
continue
for j_sym_group in j_sym_groups:
rt_mx = rt_mx_i_inv.multiply(
asu_mappings.get_rt_mx(j_seq, j_sym_group[0]))
site_ji = rt_mx * site_j
site_ji_cart = xray_structure.unit_cell(
).orthogonalize(site_ji)
vec_i = col(atom.xyz)
vec_ji = col(site_ji_cart)
dxyz = abs(vec_i - vec_ji)
if (nearest_contact is None) or (dxyz <
nearest_contact):
nearest_contact = dxyz
nearest_atom = atom_info(pdb_atom=atom_j,
symop=rt_mx)
w = water(pdb_atom=atom,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
occupancy=occupancies[i_seq],
nearest_contact=nearest_contact,
nearest_atom=nearest_atom,
score=map_stats.two_fofc_ccs[i_seq],
fmodel=map_stats.fmodel_values[i_seq],
two_fofc=map_stats.two_fofc_values[i_seq],
fofc=map_stats.fofc_values[i_seq],
anom=map_stats.anom_values[i_seq],
n_hbonds=None) # TODO
if (w.is_bad_water()):
w.outlier = True
self.n_bad += 1
elif (w.is_heavy_atom()):
w.outlier = True
self.n_heavy += 1
if (w.outlier) or (collect_all):
self.results.append(w)
self.n_outliers = len(self.results)
def __init__ (self, pdb_hierarchy, xray_structure, fmodel,
distance_cutoff=4.0, collect_all=True) :
validation.__init__(self)
from mmtbx.real_space_correlation import extract_map_stats_for_single_atoms
from cctbx import adptbx
from scitbx.matrix import col
self.n_bad = 0
self.n_heavy = 0
pdb_atoms = pdb_hierarchy.atoms()
if(len(pdb_atoms)>1):
assert (not pdb_atoms.extract_i_seq().all_eq(0))
unit_cell = xray_structure.unit_cell()
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff = distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_cart = xray_structure.sites_cart()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("resname HOH and name O")
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=fmodel,
selection=water_sel)
waters = []
for i_seq, atom in enumerate(pdb_atoms) :
if (water_sel[i_seq]) :
rt_mx_i_inv = asu_mappings.get_rt_mx(i_seq, 0).inverse()
self.n_total += 1
asu_dict = asu_table[i_seq]
nearest_atom = nearest_contact = None
for j_seq, j_sym_groups in asu_dict.items() :
atom_j = pdb_atoms[j_seq]
site_j = sites_frac[j_seq]
# Filter out hydrogens
if atom_j.element.upper().strip() in ["H", "D"]:
continue
for j_sym_group in j_sym_groups:
rt_mx = rt_mx_i_inv.multiply(asu_mappings.get_rt_mx(j_seq,
j_sym_group[0]))
site_ji = rt_mx * site_j
site_ji_cart = xray_structure.unit_cell().orthogonalize(site_ji)
vec_i = col(atom.xyz)
vec_ji = col(site_ji_cart)
dxyz = abs(vec_i - vec_ji)
if (nearest_contact is None) or (dxyz < nearest_contact) :
nearest_contact = dxyz
nearest_atom = atom_info(pdb_atom=atom_j, symop=rt_mx)
w = water(
pdb_atom=atom,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
occupancy=occupancies[i_seq],
nearest_contact=nearest_contact,
nearest_atom=nearest_atom,
score=map_stats.two_fofc_ccs[i_seq],
fmodel=map_stats.fmodel_values[i_seq],
two_fofc=map_stats.two_fofc_values[i_seq],
fofc=map_stats.fofc_values[i_seq],
anom=map_stats.anom_values[i_seq],
n_hbonds=None) # TODO
if (w.is_bad_water()) :
w.outlier = True
self.n_bad += 1
elif (w.is_heavy_atom()) :
w.outlier = True
self.n_heavy += 1
if (w.outlier) or (collect_all) :
self.results.append(w)
self.n_outliers = len(self.results)
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)
