def noise_filtered_map_coefficients(self, map_coefficients):
from mmtbx.maps import fem
f_map = self.fmodel.electron_density_map().map_coefficients(
map_type="2mFo-DFc",
isotropize=True,
exclude_free_r_reflections=False,
fill_missing=True)
selection = fem.good_atoms_selection(
crystal_gridding=self.crystal_gridding,
map_coeffs=f_map, #map_coefficients,
xray_structure=self.fmodel.xray_structure)
fft_map = cctbx.miller.fft_map(crystal_gridding=self.crystal_gridding,
fourier_coefficients=map_coefficients)
fft_map.apply_sigma_scaling()
m = fft_map.real_map_unpadded()
m = fem.low_volume_density_elimination(m=m,
fmodel=self.fmodel,
selection=selection,
end=11)
### Filter by 2mFo-DFc filled map
fft_map = cctbx.miller.fft_map(crystal_gridding=self.crystal_gridding,
fourier_coefficients=f_map)
fft_map.apply_sigma_scaling()
filter_mask = fft_map.real_map_unpadded()
filter_mask = fem.low_volume_density_elimination(m=filter_mask,
fmodel=self.fmodel,
selection=selection,
end=6) #11)
sel = filter_mask < 0.25
filter_mask = filter_mask.set_selected(sel, 0)
sel = filter_mask >= 0.25
filter_mask = filter_mask.set_selected(sel, 1)
###
return map_coefficients.structure_factors_from_map(
map=m * filter_mask,
use_scale=True,
anomalous_flag=False,
use_sg=False)
def noise_filtered_map_coefficients(self, map_coefficients):
from mmtbx.maps import fem
f_map = self.fmodel.electron_density_map().map_coefficients(
map_type = "2mFo-DFc",
isotropize = True,
exclude_free_r_reflections = False,
fill_missing = True)
selection = fem.good_atoms_selection(
crystal_gridding = self.crystal_gridding,
map_coeffs = f_map,#map_coefficients,
xray_structure = self.fmodel.xray_structure)
fft_map = cctbx.miller.fft_map(
crystal_gridding = self.crystal_gridding,
fourier_coefficients = map_coefficients)
fft_map.apply_sigma_scaling()
m = fft_map.real_map_unpadded()
m = fem.low_volume_density_elimination(m=m, fmodel=self.fmodel,
selection=selection, end=11)
### Filter by 2mFo-DFc filled map
fft_map = cctbx.miller.fft_map(
crystal_gridding = self.crystal_gridding,
fourier_coefficients = f_map)
fft_map.apply_sigma_scaling()
filter_mask = fft_map.real_map_unpadded()
filter_mask = fem.low_volume_density_elimination(m=filter_mask,
fmodel=self.fmodel, selection=selection, end=6)#11)
sel = filter_mask<0.25
filter_mask = filter_mask.set_selected(sel, 0)
sel = filter_mask>=0.25
filter_mask = filter_mask.set_selected(sel, 1)
###
return map_coefficients.structure_factors_from_map(
map = m*filter_mask,
use_scale = True,
anomalous_flag = False,
use_sg = False)