def __init__(self,
crystal_gridding,
fmodel,
map_type,
max_boxes,
box_size_as_fraction=None):
sgt = fmodel.f_obs().space_group().type()
assert sgt.number() == 1
def get_map(fmodel, map_type, external_complete_set=None):
f_map = fmodel.electron_density_map().map_coefficients(
map_type=map_type, isotropize=True, fill_missing=False)
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_map)
return fft_map.real_map_unpadded()
f_model = fmodel.f_model_scaled_with_k1()
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_model)
f_model_map_data = fft_map.real_map_unpadded()
zero_complex_ma = f_model.customized_copy(
data=flex.complex_double(f_model.data().size(), 0))
b = maptbx.boxes(fraction=0.3,
n_real=f_model_map_data.focus(),
max_boxes=max_boxes,
log=sys.stdout)
self.map_result = flex.double(flex.grid(b.n_real))
self.r = flex.double()
for s, e in zip(b.starts, b.ends):
f_model_map_data_omit = maptbx.set_box_copy(
value=0, map_data_to=f_model_map_data, start=s, end=e)
f_model_omit = f_model.structure_factors_from_map(
map=f_model_map_data_omit,
use_scale=True,
anomalous_flag=False,
use_sg=False)
fmodel_ = mmtbx.f_model.manager(f_obs=fmodel.f_obs(),
r_free_flags=fmodel.r_free_flags(),
f_calc=f_model_omit,
f_mask=zero_complex_ma)
self.r.append(fmodel_.r_work())
f_map_data = get_map(fmodel=fmodel_, map_type=map_type)
etmp = [e[0] - 1, e[1] - 1,
e[2] - 1] # because .copy() includes right edge
box = maptbx.copy(f_map_data, s, etmp)
box.reshape(flex.grid(box.all()))
maptbx.set_box(map_data_from=box,
map_data_to=self.map_result,
start=s,
end=e)
sd = self.map_result.sample_standard_deviation()
self.map_result = self.map_result / sd
self.map_coefficients = fmodel.f_obs().structure_factors_from_map(
map=self.map_result,
use_scale=True,
anomalous_flag=False,
use_sg=False)
def run_0(symbol="C 2"):
space_group_info = sgtbx.space_group_info(symbol=symbol)
xrs = random_structure.xray_structure(space_group_info=space_group_info,
elements=["N"] * 50,
volume_per_atom=100.0,
random_u_iso=True)
#
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=xrs.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
#
F = xrs.structure_factors(d_min=1.5).f_calc()
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
#
bin_selections = []
F.setup_binner(reflections_per_bin=50)
for i_bin in F.binner().range_used():
sel = F.binner().selection(i_bin)
bin_selections.append(sel)
#
d_spacings = F.d_spacings().data()
ss = 1. / flex.pow2(d_spacings) / 4.
k_mask_tmp = mmtbx.f_model.ext.k_mask(ss, 0.35, 80.)
k_mask = flex.double(F.data().size(), 0)
k_isotropic = flex.double(F.data().size(), 0)
for s in bin_selections:
d = d_spacings.select(s)
k_mask.set_selected(s, flex.mean(k_mask_tmp.select(s)))
k_isotropic.set_selected(s, random.randint(1, 10))
#
fmodel = mmtbx.f_model.manager(xray_structure=xrs,
f_obs=abs(F),
k_isotropic=k_isotropic,
k_anisotropic=k_anisotropic,
k_mask=k_mask)
f_calc = fmodel.f_calc()
f_masks = fmodel.f_masks()
f_model = fmodel.f_model()
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags(use_lattice_symmetry=False)
#
assert approx_equal(bulk_solvent.r_factor(f_obs.data(), f_model.data()), 0)
aso = scaler.run(f_obs=f_obs,
f_calc=f_calc,
f_mask=f_masks,
r_free_flags=r_free_flags,
bin_selections=bin_selections,
number_of_cycles=500,
auto_convergence_tolerance=1.e-9,
ss=ss,
try_poly=True,
try_expanal=True,
try_expmin=True,
verbose=True)
print("r_f:", aso.r_final)
print("r_l:", aso.r_low)
print("r_h:", aso.r_high)
assert aso.r_final < 0.0009, [aso.r_final, 0.0009]
assert aso.r_low < 0.0017, [aso.r_low, 0.0017]
assert aso.r_high < 0.0006, [aso.r_high, 0.0006]
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(),
abs(aso.core.f_model).data(), 1),
bulk_solvent.r_factor(f_obs.data(),
abs(aso.core.f_model).data()))
def run_0(symbol = "C 2"):
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*50,
volume_per_atom = 100.0,
random_u_iso = True)
#
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=xrs.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
#
F = xrs.structure_factors(d_min = 1.5).f_calc()
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
#
bin_selections = []
F.setup_binner(reflections_per_bin=50)
for i_bin in F.binner().range_used():
sel = F.binner().selection(i_bin)
bin_selections.append(sel)
#
d_spacings = F.d_spacings().data()
ss = 1./flex.pow2(d_spacings) / 4.
k_mask_tmp = mmtbx.f_model.ext.k_mask(ss, 0.35, 80.)
k_mask = flex.double(F.data().size(), 0)
k_isotropic = flex.double(F.data().size(), 0)
for s in bin_selections:
d = d_spacings.select(s)
k_mask.set_selected(s, flex.mean(k_mask_tmp.select(s)))
k_isotropic.set_selected(s, random.randint(1,10))
#
fmodel = mmtbx.f_model.manager(
xray_structure = xrs,
f_obs = abs(F),
k_isotropic = k_isotropic,
k_anisotropic = k_anisotropic,
k_mask = k_mask)
f_calc = fmodel.f_calc()
f_masks = fmodel.f_masks()
f_model = fmodel.f_model()
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags(use_lattice_symmetry=False)
#
assert approx_equal(bulk_solvent.r_factor(f_obs.data(), f_model.data()), 0)
aso = scaler.run(
f_obs = f_obs,
f_calc = f_calc,
f_mask = f_masks,
r_free_flags = r_free_flags,
bin_selections = bin_selections,
number_of_cycles = 500,
auto_convergence_tolerance = 1.e-9,
ss = ss,
try_poly = True,
try_expanal = True,
try_expmin = True,
verbose = False)
assert approx_equal(aso.r_final, 0.00037, 0.00001)
assert approx_equal(aso.r_low, 0.00002, 0.00001)
assert approx_equal(aso.r_high, 0.00006, 0.00001)
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data(), 1),
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data()))
def __init__(
self,
crystal_gridding,
fmodel,
map_type,
max_boxes,
box_size_as_fraction=None):
sgt = fmodel.f_obs().space_group().type()
assert sgt.number() == 1
def get_map(fmodel, map_type, external_complete_set=None):
f_map = fmodel.electron_density_map().map_coefficients(
map_type = map_type,
isotropize = True,
fill_missing = False)
fft_map = miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_map)
return fft_map.real_map_unpadded()
f_model = fmodel.f_model_scaled_with_k1()
fft_map = miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_model)
f_model_map_data = fft_map.real_map_unpadded()
zero_complex_ma = f_model.customized_copy(
data = flex.complex_double(f_model.data().size(), 0))
b = maptbx.boxes(
fraction = 0.3,
n_real = f_model_map_data.focus(),
max_boxes=max_boxes,
log=sys.stdout)
self.map_result = flex.double(flex.grid(b.n_real))
self.r = flex.double()
for s,e in zip(b.starts, b.ends):
f_model_map_data_omit = maptbx.set_box_copy(
value = 0,
map_data_to = f_model_map_data,
start = s,
end = e)
f_model_omit = f_model.structure_factors_from_map(
map = f_model_map_data_omit,
use_scale = True,
anomalous_flag = False,
use_sg = False)
fmodel_ = mmtbx.f_model.manager(
f_obs = fmodel.f_obs(),
r_free_flags = fmodel.r_free_flags(),
f_calc = f_model_omit,
f_mask = zero_complex_ma)
self.r.append(fmodel_.r_work())
f_map_data = get_map(fmodel=fmodel_, map_type=map_type)
etmp = [e[0]-1, e[1]-1, e[2]-1] # because .copy() includes right edge
box = maptbx.copy(f_map_data, s, etmp)
box.reshape(flex.grid(box.all()))
maptbx.set_box(
map_data_from = box,
map_data_to = self.map_result,
start = s,
end = e)
sd = self.map_result.sample_standard_deviation()
self.map_result = self.map_result/sd
self.map_coefficients = fmodel.f_obs().structure_factors_from_map(
map = self.map_result,
use_scale = True,
anomalous_flag = False,
use_sg = False)
