def exercise():
""" Compare simple mask (mmtbx/utils.h) with classic mask. Does not account
for site multiplicity due to symmetry. Also, this is an alternative
exercise for asu mask.
"""
for i_pdb, pdb_str in enumerate([pdb_str_1, pdb_str_2, pdb_str_3]):
for solvent_radius in [0, 1.0]:
print "file %d solvent_raius: %3.1f"%(i_pdb, solvent_radius)
xrs = iotbx.pdb.input(source_info = None,
lines = pdb_str).xray_structure_simple()
mp = mmtbx.masks.mask_master_params.extract()
mp.solvent_radius=solvent_radius
mp.shrink_truncation_radius=0.0
mmtbx_masks_asu_mask_obj = mmtbx.masks.asu_mask(
xray_structure = xrs.expand_to_p1(sites_mod_positive=True), # Must be P1
d_min = 1,
mask_params = mp)
mask_data = mmtbx_masks_asu_mask_obj.mask_data_whole_uc()
c1o,c0o,s,csf = mask_data.count(1), mask_data.count(0), mask_data.size(),\
mmtbx_masks_asu_mask_obj.asu_mask.contact_surface_fraction
assert c1o+c0o==s
f1o, f0o = c1o*100./s, c0o*100./s
print " old", f1o, f0o, csf
mask_data = maptbx.mask(
xray_structure = xrs, # Expanded to P1 internally
n_real = mask_data.focus(),
solvent_radius = solvent_radius)
c1n, c0n, s = mask_data.count(1), mask_data.count(0), mask_data.size()
assert c1n+c0n==s
f1n, f0n = c1n*100./s, c0n*100./s
print " new:", f1n, f0n
assert approx_equal(f1o, f1n, 1)
assert approx_equal(f0o, f0n, 1)
assert approx_equal(f1o, csf*100, 1)
def prepare_user_map(self):
print >> self.log, "Preparing user map..."
self.map_shift_manager = mmtbx.utils.shift_origin(
map_data=self.user_supplied_map,
xray_structure=self.model.get_xray_structure(),
crystal_symmetry=self.cs)
if (self.map_shift_manager.shift_cart is not None):
# Need to figure out way to save the shift to shift back
# and apply it to whole_pdb, master_pdb, etc. Don't forget about
# boxing hierarchy when symmetry is not available or corrupted...
raise Sorry(
"Map origin is not at (0,0,0). This is not implemented for model_idealization"
)
map_data = self.map_shift_manager.map_data
self.reference_map = map_data
self.master_map = self.reference_map.deep_copy()
if self.model.ncs_constraints_present():
mask = maptbx.mask(
xray_structure=self.model.get_xray_structure().select(
self.model.get_master_selection()),
n_real=self.master_map.focus(),
mask_value_inside_molecule=1,
mask_value_outside_molecule=-1,
solvent_radius=0,
atom_radius=1.)
self.master_map = self.reference_map * mask
if self.params.debug:
iotbx.ccp4_map.write_ccp4_map(
file_name="%s_3_master.map" % self.params.output_prefix,
unit_cell=self.cs.unit_cell(),
space_group=self.cs.space_group(),
map_data=self.master_map,
labels=flex.std_string([""]))
self.master_map = map_data
def prepare_reference_map_3(self):
""" with ramachandran outliers """
xrs = self.model.get_xray_structure().deep_copy_scatterers()
pdb_h = self.model.get_hierarchy()
print("Preparing reference map, method 3", file=self.log)
outlier_selection_txt = mmtbx.building.loop_closure.utils. \
rama_score_selection(pdb_h, self.model.get_ramachandran_manager(), "outlier",1)
asc = self.model.get_atom_selection_cache()
# print >> self.log, "rama outlier selection:", outlier_selection_txt
rama_out_sel = asc.selection(outlier_selection_txt)
xrs=xrs.set_b_iso(value=50)
# side_chain_no_cb_selection = ~ xrs.main_chain_selection()
side_chain_no_cb_selection = ~ xrs.backbone_selection()
xrs = xrs.set_b_iso(value=200, selection=side_chain_no_cb_selection)
xrs = xrs.set_b_iso(value=150, selection=rama_out_sel)
# xrs = xrs.set_occupancies(value=0.3, selection=rama_out_sel)
crystal_gridding = maptbx.crystal_gridding(
unit_cell = xrs.unit_cell(),
space_group_info = xrs.space_group_info(),
symmetry_flags = maptbx.use_space_group_symmetry,
d_min = self.params.reference_map_resolution)
fc = xrs.structure_factors(
d_min = self.params.reference_map_resolution,
algorithm = "direct").f_calc()
fft_map = miller.fft_map(
crystal_gridding=crystal_gridding,
fourier_coefficients=fc)
fft_map.apply_sigma_scaling()
self.reference_map = fft_map.real_map_unpadded(in_place=False)
if self.params.debug:
fft_map.as_xplor_map(file_name="%s_3.map" % self.params.output_prefix)
self.master_map = self.reference_map.deep_copy()
if self.model.ncs_constraints_present():
# here we are negating non-master part of the model
# self.master_sel=master_sel
# self.master_map = self.reference_map.deep_copy()
mask = maptbx.mask(
xray_structure=xrs.select(self.model.get_master_selection()),
n_real=self.master_map.focus(),
mask_value_inside_molecule=1,
mask_value_outside_molecule=-1,
solvent_radius=0,
atom_radius=1.)
self.master_map = self.reference_map * mask
if self.params.debug:
iotbx.mrcfile.write_ccp4_map(
file_name="%s_3_master.map" % self.params.output_prefix,
unit_cell=xrs.unit_cell(),
space_group=xrs.space_group(),
map_data=self.master_map,
labels=flex.std_string([""]))
def exercise():
""" Compare simple mask (maptbx/mask.h) with classic mask. Does not account
for site multiplicity due to symmetry. Also, this is an alternative
exercise for asu mask.
"""
for i_pdb, pdb_str in enumerate([pdb_str_1, pdb_str_2, pdb_str_3]):
for solvent_radius in [0, 1.0]:
print("file %d solvent_raius: %3.1f" % (i_pdb, solvent_radius))
xrs = iotbx.pdb.input(source_info=None,
lines=pdb_str).xray_structure_simple()
mp = mmtbx.masks.mask_master_params.extract()
mp.solvent_radius = solvent_radius
mp.shrink_truncation_radius = 0.0
mp.grid_step_factor = 4
mmtbx_masks_asu_mask_obj = mmtbx.masks.asu_mask(
xray_structure=xrs.expand_to_p1(
sites_mod_positive=True), # Must be P1
d_min=1,
mask_params=mp)
mask_data = mmtbx_masks_asu_mask_obj.mask_data_whole_uc()
c1o,c0o,s,csf = mask_data.count(1), mask_data.count(0), mask_data.size(),\
mmtbx_masks_asu_mask_obj.asu_mask.contact_surface_fraction
assert c1o + c0o == s
f1o, f0o = c1o * 100. / s, c0o * 100. / s
print(" old", f1o, f0o, csf)
mask_data = maptbx.mask(
xray_structure=xrs, # Expanded to P1 internally
n_real=mask_data.focus(),
solvent_radius=solvent_radius)
c1n, c0n, s = mask_data.count(1), mask_data.count(
0), mask_data.size()
assert c1n + c0n == s
f1n, f0n = c1n * 100. / s, c0n * 100. / s
print(" new:", f1n, f0n)
assert approx_equal(f1o, f1n, 1)
assert approx_equal(f0o, f0n, 1)
assert approx_equal(f1o, csf * 100, 1)
