def _compute_d99(self):
if (not self.params.compute.d99): return
d99 = maptbx.d99(f_map=self.f_map)
self.d99 = d99.result.d99
d99_obj_1, d99_obj_2 = None, None
if (self.map_data_1 is not None):
d99_1 = maptbx.d99(map=self.map_data_1,
crystal_symmetry=self.crystal_symmetry)
d99_2 = maptbx.d99(map=self.map_data_2,
crystal_symmetry=self.crystal_symmetry)
self.d99_1 = d99_1.result.d99
self.d99_2 = d99_2.result.d99
self.f_map_1 = d99_1.f_map
self.f_map_2 = d99_2.f_map
def get_atom_radius(xray_structure=None,
d_min=None,
map_data=None,
crystal_symmetry=None,
radius=None):
if (radius is not None): return radius
radii = []
if (d_min is not None):
radii.append(d_min)
if ([xray_structure, crystal_symmetry].count(None) == 0):
assert crystal_symmetry.is_similar_symmetry(
xray_structure.crystal_symmetry())
if ([map_data, crystal_symmetry].count(None) == 0):
d99 = maptbx.d99(map=map_data,
crystal_symmetry=crystal_symmetry).result.d99
radii.append(d99)
if (xray_structure is not None and d_min is not None):
b_iso = adptbx.u_as_b(
flex.mean(xray_structure.extract_u_iso_or_u_equiv()))
o = maptbx.atom_curves(scattering_type="C",
scattering_table="electron")
rad_image = o.image(d_min=d_min,
b_iso=b_iso,
radius_max=max(15., d_min),
radius_step=0.01).radius
radii.append(rad_image)
return max(3, min(10, max(radii)))
def _compute_d99(self):
if (not self.params.compute_d99): return
d99_obj = maptbx.d99(map=self.map_data,
crystal_symmetry=self.crystal_symmetry)
self.d9 = d99_obj.result.d9
self.d99 = d99_obj.result.d99
self.d999 = d99_obj.result.d999
self.f = d99_obj.f
d99_obj_1, d99_obj_2 = None, None
if (self.half_map_data_1 is not None):
d99_obj_1 = maptbx.d99(map=self.half_map_data_1,
crystal_symmetry=self.crystal_symmetry)
d99_obj_2 = maptbx.d99(map=self.half_map_data_2,
crystal_symmetry=self.crystal_symmetry)
self.d99_1 = d99_obj_1.result.d99
self.d99_2 = d99_obj_2.result.d99
self.f1 = d99_obj_1.f
self.f2 = d99_obj_2.f
def _compute_d99(self):
if (not self.params.compute.d99): return
d99 = maptbx.d99(f_map=self.f_map)
self.d99 = d99.result.d99
self.d999 = d99.result.d999
self.d9999 = d99.result.d9999
self.f_map = self.f_map.resolution_filter(d_min=self.d9999 -
0.1) # TRUNCATED!
d99_obj_1, d99_obj_2 = None, None
if (self.base.half_map_data_1() is not None):
d99_1 = maptbx.d99(map=self.base.half_map_data_1(),
crystal_symmetry=self.base.crystal_symmetry())
d99_2 = maptbx.d99(map=self.base.half_map_data_2(),
crystal_symmetry=self.base.crystal_symmetry())
self.d99_1 = d99_1.result.d99
self.d99_2 = d99_2.result.d99
self.f_map_1 = d99_1.f_map
self.f_map_2 = d99_2.f_map
def _compute_radius(self):
if (not self.params.mask_maps): return
if (self.xray_structure is None): return
if (self.xray_structure is not None
and [self.radius_smooth, self.resolution].count(None) == 2):
f_map = miller.structure_factor_box_from_map(
map=self.map_data, crystal_symmetry=self.crystal_symmetry)
self.radius_smooth = maptbx.d99(f_map=f_map).result.d99
self.radius_smooth = get_atom_radius(
xray_structure=self.xray_structure,
radius=self.radius_smooth,
resolution=self.resolution)
def exercise_d99():
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
ph = pdb_inp.construct_hierarchy()
xrs = ph.extract_xray_structure(
crystal_symmetry=pdb_inp.crystal_symmetry())
crystal_gridding = maptbx.crystal_gridding(
unit_cell=xrs.unit_cell(),
space_group_info=xrs.space_group_info(),
resolution_factor=0.25,
d_min=2.,
symmetry_flags=maptbx.use_space_group_symmetry)
fc = xrs.structure_factors(d_min=2.).f_calc()
fft_map = fc.fft_map(crystal_gridding=crystal_gridding)
map = fft_map.real_map_unpadded()
#
o = maptbx.d99(map=map, crystal_symmetry=xrs.crystal_symmetry())
assert approx_equal(o.result.d999, 2.0, 0.03)
def show_cc(map_data, xray_structure, log=None):
import mmtbx.maps.mtriage
from mmtbx.maps.correlation import five_cc
xrs = xray_structure
xrs.scattering_type_registry(table="electron")
d99 = maptbx.d99(map=map_data,
crystal_symmetry=xrs.crystal_symmetry()).result.d99
if (log is not None): print("Resolution of map is: %6.4f" % d99, file=log)
result = five_cc(map=map_data,
xray_structure=xrs,
d_min=d99,
compute_cc_box=False,
compute_cc_mask=True,
compute_cc_peaks=False,
compute_cc_volume=False).result
if (log is not None):
print("Map-model correlation coefficient (CC)", file=log)
print(" CC_mask : %6.4f" % result.cc_mask, file=log)
return result.cc_mask
