def f_calc_symmetrisations(f_obs, f_calc_in_p1, min_cc_peak_height):
# The fast correlation map as per cctbx.translation_search.fast_nv1995
# is computed and its peaks studied.
# Inspiration from phenix.substructure.hyss for the parameters tuning.
if 0: # Display f_calc_in_p1
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="f_calc in P1 before fast CC",
fft_map=f_calc_in_p1.fft_map(),
iso_level_positive_range_fraction=0.8)
crystal_gridding = f_obs.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=False),
resolution_factor=1/3
)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc_in_p1.indices(),
p1_f_calc=f_calc_in_p1.data()).target_map()
if 0: # Display correlation_map
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="Fast CC map",
raw_map=correlation_map,
unit_cell=f_calc_in_p1.unit_cell(),
positive_iso_level=0.8)
search_parameters = maptbx.peak_search_parameters(
peak_search_level=1,
peak_cutoff=0.5,
interpolate=True,
min_distance_sym_equiv=1e-6,
general_positions_only=False,
min_cross_distance=f_obs.d_min()/2)
## The correlation map is not a miller.fft_map, just a 3D flex.double
correlation_map_peaks = crystal_gridding.tags().peak_search(
map=correlation_map,
parameters=search_parameters)
# iterate over the strong peak; for each, shift and symmetrised f_calc
for peak in correlation_map_peaks:
if peak.height < min_cc_peak_height: break
sr = symmetry_search.shift_refinement(
f_obs, f_calc_in_p1, peak.site)
yield sr.symmetrised_shifted_sf.f_x, sr.shift, sr.goos.correlation
def f_calc_symmetrisations(f_obs, f_calc_in_p1, min_cc_peak_height):
# The fast correlation map as per cctbx.translation_search.fast_nv1995
# is computed and its peaks studied.
# Inspiration from phenix.substructure.hyss for the parameters tuning.
if 0: # Display f_calc_in_p1
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="f_calc in P1 before fast CC",
fft_map=f_calc_in_p1.fft_map(),
iso_level_positive_range_fraction=0.8)
crystal_gridding = f_obs.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False, have_f_part=False),
resolution_factor=1 / 3)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc_in_p1.indices(),
p1_f_calc=f_calc_in_p1.data()).target_map()
if 0: # Display correlation_map
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="Fast CC map",
raw_map=correlation_map,
unit_cell=f_calc_in_p1.unit_cell(),
positive_iso_level=0.8)
search_parameters = maptbx.peak_search_parameters(
peak_search_level=1,
peak_cutoff=0.5,
interpolate=True,
min_distance_sym_equiv=1e-6,
general_positions_only=False,
min_cross_distance=f_obs.d_min() / 2)
## The correlation map is not a miller.fft_map, just a 3D flex.double
correlation_map_peaks = crystal_gridding.tags().peak_search(
map=correlation_map, parameters=search_parameters)
# iterate over the strong peak; for each, shift and symmetrised f_calc
for peak in correlation_map_peaks:
if peak.height < min_cc_peak_height: break
sr = symmetry_search.shift_refinement(f_obs, f_calc_in_p1, peak.site)
yield sr.symmetrised_shifted_sf.f_x, sr.shift, sr.goos.correlation