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)