def find_and_build_ions (
manager,
fmodels,
model,
wavelength,
params,
nproc=1,
elements=Auto,
out=None,
run_ordered_solvent=False,
occupancy_strategy_enabled=False,
group_anomalous_strategy_enabled=False,
use_svm=None) :
"""
Analyzes the water molecules in a structure and re-labels them as ions if
they scatter and bind environments that we expect of that ion.
Parameters
----------
manager : mmtbx.ions.identity.manager
fmodels : mmtbx.fmodels
model : mmtbx.model.manager
wavelength : float
params : libtbx.phil.scope_extract
nproc : int, optional
elements : list of str, optional
out : file, optional
run_ordered_solvent : bool, optional
occupancy_strategy_enabled : bool, optional
group_anomalous_strategy_enabled : bool, optional
use_svm : bool, optional
See Also
--------
mmtbx.ions.identify.manager.analyze_waters
"""
import mmtbx.refinement.minimization
from mmtbx.refinement.anomalous_scatterer_groups import \
get_single_atom_selection_string
from mmtbx.refinement import anomalous_scatterer_groups
import mmtbx.ions.identify
import mmtbx.ions.svm
from cctbx.eltbx import sasaki
from cctbx import crystal
from cctbx import adptbx
from cctbx import xray
from scitbx.array_family import flex
import scitbx.lbfgs
if (use_svm is None) :
use_svm = getattr(params, "use_svm", False)
assert (1.0 >= params.initial_occupancy >= 0)
fmodel = fmodels.fmodel_xray()
anomalous_flag = fmodel.f_obs().anomalous_flag()
if (out is None) : out = sys.stdout
model.xray_structure = fmodel.xray_structure
model.xray_structure.tidy_us()
pdb_hierarchy = model.pdb_hierarchy(sync_with_xray_structure=True)
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
# FIXME why does B for anisotropic waters end up negative?
u_iso = model.xray_structure.extract_u_iso_or_u_equiv()
for i_seq, atom in enumerate(pdb_atoms) :
labels = atom.fetch_labels()
if (labels.resname == "HOH") and (atom.b < 0) :
assert (u_iso[i_seq] >= 0)
atom.b = adptbx.u_as_b(u_iso[i_seq])
if (manager is None) :
manager_class = None
if (use_svm) :
manager_class = mmtbx.ions.svm.manager
if params.svm.svm_name == "merged_high_res" :
params.find_anomalous_substructure = False
params.use_phaser = False
manager = mmtbx.ions.identify.create_manager(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=model.restraints_manager.geometry,
fmodel=fmodel,
wavelength=wavelength,
params=params,
nproc=nproc,
verbose=params.debug,
log=out,
manager_class=manager_class)
else :
grm = model.restraints_manager.geometry
connectivity = grm.shell_sym_tables[0].full_simple_connectivity()
manager.update_structure(
pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
connectivity=connectivity,
log=out)
manager.update_maps()
model.update_anomalous_groups(out=out)
make_sub_header("Analyzing water molecules", out=out)
manager.show_current_scattering_statistics(out=out)
anomalous_groups = []
# XXX somehow comma-separation of phil strings fields doesn't work
if (isinstance(elements, list)) and (len(elements) == 1) :
elements = elements[0].split(",")
water_ion_candidates = manager.analyze_waters(
out=out,
candidates=elements)
modified_iselection = flex.size_t()
default_b_iso = manager.get_initial_b_iso()
# Build in the identified ions
for_building = []
if (use_svm) :
for result in water_ion_candidates :
for_building.append((result.i_seq, result.final_choice))
else :
for i_seq, final_choices, two_fofc in water_ion_candidates :
if (len(final_choices) == 1) :
for_building.append((i_seq, final_choices[0]))
skipped = []
if (len(for_building) > 0) :
make_sub_header("Adding %d ions to model" % len(for_building), out)
for k, (i_seq, final_choice) in enumerate(for_building) :
atom = manager.pdb_atoms[i_seq]
skip = False
for other_i_seq, other_ion in for_building[:k] :
if (other_i_seq in skipped) : continue
if (((other_ion.charge > 0) and (final_choice.charge > 0)) or
((other_ion.charge < 0) and (final_choice.charge < 0))) :
other_atom = manager.pdb_atoms[other_i_seq]
dxyz = atom.distance(other_atom)
if (dxyz < params.max_distance_between_like_charges) :
print >> out, \
" %s (%s%+d) is only %.3fA from %s (%s%+d), skipping for now" %\
(atom.id_str(), final_choice.element, final_choice.charge, dxyz,
other_atom.id_str(), other_ion.element, other_ion.charge)
skipped.append(i_seq)
skip = True
break
if (skip) : continue
print >> out, " %s becomes %s%+d" % \
(atom.id_str(), final_choice.element, final_choice.charge)
refine_adp = params.refine_ion_adp
if (refine_adp == "Auto") :
if (fmodel.f_obs().d_min() <= 1.5) :
refine_adp = "anisotropic"
elif (fmodel.f_obs().d_min() < 2.5) :
atomic_number = sasaki.table(final_choice.element).atomic_number()
if (atomic_number >= 19) :
refine_adp = "anisotropic"
# Modify the atom object - this is clumsy but they will be grouped into
# a single chain at the end of refinement
initial_b_iso = params.initial_b_iso
if (initial_b_iso is Auto) :
initial_b_iso = manager.guess_b_iso_real(i_seq)
element = final_choice.element
if (element == "IOD") : # FIXME
element = "I"
modified_atom = model.convert_atom(
i_seq=i_seq,
scattering_type=final_choice.scattering_type(),
atom_name=element,
element=element,
charge=final_choice.charge,
residue_name=final_choice.element,
initial_occupancy=params.initial_occupancy,
initial_b_iso=initial_b_iso,
chain_id=params.ion_chain_id,
segid="ION",
refine_adp=refine_adp,
refine_occupancies=False) #params.refine_ion_occupancies)
if (params.refine_anomalous) and (anomalous_flag) :
scatterer = model.xray_structure.scatterers()[i_seq]
if (wavelength is not None) :
fp_fdp_info = sasaki.table(final_choice.element).at_angstrom(
wavelength)
scatterer.fp = fp_fdp_info.fp()
scatterer.fdp = fp_fdp_info.fdp()
print >> out, " setting f'=%g, f''=%g" % (scatterer.fp,
scatterer.fdp)
group = xray.anomalous_scatterer_group(
iselection=flex.size_t([i_seq]),
f_prime=scatterer.fp,
f_double_prime=scatterer.fdp,
refine=["f_prime","f_double_prime"],
selection_string=get_single_atom_selection_string(modified_atom),
update_from_selection=True)
anomalous_groups.append(group)
modified_iselection.append(i_seq)
if (len(modified_iselection) > 0) :
scatterers = model.xray_structure.scatterers()
# FIXME not sure this is actually working as desired...
site_symmetry_table = model.xray_structure.site_symmetry_table()
for i_seq in site_symmetry_table.special_position_indices() :
scatterers[i_seq].site = crystal.correct_special_position(
crystal_symmetry=model.xray_structure,
special_op=site_symmetry_table.get(i_seq).special_op(),
site_frac=scatterers[i_seq].site,
site_label=scatterers[i_seq].label,
tolerance=1.0)
model.xray_structure.replace_scatterers(scatterers=scatterers)
def show_r_factors () :
return "r_work=%6.4f r_free=%6.4f" % (fmodel.r_work(), fmodel.r_free())
fmodel.update_xray_structure(
xray_structure=model.xray_structure,
update_f_calc=True,
update_f_mask=True)
n_anom = len(anomalous_groups)
refine_anomalous = anomalous_flag and params.refine_anomalous and n_anom>0
refine_occupancies = ((params.refine_ion_occupancies or refine_anomalous)
and ((not occupancy_strategy_enabled) or
(model.refinement_flags.s_occupancies is None) or
(len(model.refinement_flags.s_occupancies) == 0)))
if (refine_anomalous) :
if ((model.anomalous_scatterer_groups is not None) and
(group_anomalous_strategy_enabled)) :
model.anomalous_scatterer_groups.extend(anomalous_groups)
refine_anomalous = False
if (refine_occupancies) or (refine_anomalous) :
print >> out, ""
print >> out, " occupancy refinement (new ions only): start %s" % \
show_r_factors()
fmodel.xray_structure.scatterers().flags_set_grads(state = False)
fmodel.xray_structure.scatterers().flags_set_grad_occupancy(
iselection = modified_iselection)
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = 25)
minimized = mmtbx.refinement.minimization.lbfgs(
restraints_manager = None,
fmodels = fmodels,
model = model,
is_neutron_scat_table = False,
lbfgs_termination_params = lbfgs_termination_params)
fmodel.xray_structure.adjust_occupancy(
occ_max = 1.0,
occ_min = 0,
selection = modified_iselection)
zero_occ = []
for i_seq in modified_iselection :
occ = fmodel.xray_structure.scatterers()[i_seq].occupancy
if (occ == 0) :
zero_occ.append(i_seq)
fmodel.update_xray_structure(
update_f_calc=True,
update_f_mask=True)
print >> out, " final %s" % \
show_r_factors()
if (len(zero_occ) > 0) :
print >> out, " WARNING: occupancy dropped to zero for %d atoms:"
atoms = model.pdb_hierarchy().atoms()
for i_seq in zero_occ :
print >> out, " %s" % atoms[i_seq].id_str(suppress_segid=True)
print >> out, ""
if (refine_anomalous) :
assert fmodel.f_obs().anomalous_flag()
print >> out, " anomalous refinement (new ions only): start %s" % \
show_r_factors()
fmodel.update(target_name="ls")
anomalous_scatterer_groups.minimizer(
fmodel=fmodel,
groups=anomalous_groups)
fmodel.update(target_name="ml")
print >> out, " final %s" % \
show_r_factors()
print >> out, ""
return manager
def find_and_build_ions(manager,
fmodels,
model,
wavelength,
params,
nproc=1,
elements=Auto,
out=None,
run_ordered_solvent=False,
occupancy_strategy_enabled=False,
group_anomalous_strategy_enabled=False,
use_svm=None):
"""
Analyzes the water molecules in a structure and re-labels them as ions if
they scatter and bind environments that we expect of that ion.
Parameters
----------
manager : mmtbx.ions.identity.manager
fmodels : mmtbx.fmodels
model : mmtbx.model.manager
wavelength : float
params : libtbx.phil.scope_extract
nproc : int, optional
elements : list of str, optional
out : file, optional
run_ordered_solvent : bool, optional
occupancy_strategy_enabled : bool, optional
group_anomalous_strategy_enabled : bool, optional
use_svm : bool, optional
See Also
--------
mmtbx.ions.identify.manager.analyze_waters
"""
import mmtbx.refinement.minimization
from mmtbx.refinement.anomalous_scatterer_groups import \
get_single_atom_selection_string
from mmtbx.refinement import anomalous_scatterer_groups
import mmtbx.ions.identify
import mmtbx.ions.svm
from cctbx.eltbx import sasaki
from cctbx import crystal
from cctbx import adptbx
from cctbx import xray
from scitbx.array_family import flex
import scitbx.lbfgs
if (use_svm is None):
use_svm = getattr(params, "use_svm", False)
assert (1.0 >= params.initial_occupancy >= 0)
fmodel = fmodels.fmodel_xray()
anomalous_flag = fmodel.f_obs().anomalous_flag()
if (out is None): out = sys.stdout
model.set_xray_structure(fmodel.xray_structure)
model.get_xray_structure().tidy_us()
pdb_hierarchy = model.get_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
# FIXME why does B for anisotropic waters end up negative?
u_iso = model.get_xray_structure().extract_u_iso_or_u_equiv()
for i_seq, atom in enumerate(pdb_atoms):
labels = atom.fetch_labels()
if (labels.resname == "HOH") and (atom.b < 0):
assert (u_iso[i_seq] >= 0)
atom.b = adptbx.u_as_b(u_iso[i_seq])
if (manager is None):
manager_class = None
if (use_svm):
manager_class = mmtbx.ions.svm.manager
if params.svm.svm_name == "merged_high_res":
params.find_anomalous_substructure = False
params.use_phaser = False
manager = mmtbx.ions.identify.create_manager(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=model.restraints_manager.geometry,
fmodel=fmodel,
wavelength=wavelength,
params=params,
nproc=nproc,
verbose=params.debug,
log=out,
manager_class=manager_class)
else:
grm = model.get_restraints_manager().geometry
connectivity = grm.shell_sym_tables[0].full_simple_connectivity()
manager.update_structure(pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
connectivity=connectivity,
log=out)
manager.update_maps()
model.update_anomalous_groups(out=out)
make_sub_header("Analyzing water molecules", out=out)
manager.show_current_scattering_statistics(out=out)
anomalous_groups = []
# XXX somehow comma-separation of phil strings fields doesn't work
if (isinstance(elements, list)) and (len(elements) == 1):
elements = elements[0].split(",")
water_ion_candidates = manager.analyze_waters(out=out, candidates=elements)
modified_iselection = flex.size_t()
default_b_iso = manager.get_initial_b_iso()
# Build in the identified ions
for_building = []
if (use_svm):
for result in water_ion_candidates:
for_building.append((result.i_seq, result.final_choice))
else:
for i_seq, final_choices, two_fofc in water_ion_candidates:
if (len(final_choices) == 1):
for_building.append((i_seq, final_choices[0]))
skipped = []
if (len(for_building) > 0):
make_sub_header("Adding %d ions to model" % len(for_building), out)
for k, (i_seq, final_choice) in enumerate(for_building):
atom = manager.pdb_atoms[i_seq]
skip = False
for other_i_seq, other_ion in for_building[:k]:
if (other_i_seq in skipped): continue
if (((other_ion.charge > 0) and (final_choice.charge > 0)) or
((other_ion.charge < 0) and (final_choice.charge < 0))):
other_atom = manager.pdb_atoms[other_i_seq]
dxyz = atom.distance(other_atom)
if (dxyz < params.max_distance_between_like_charges):
print(" %s (%s%+d) is only %.3fA from %s (%s%+d), skipping for now" %\
(atom.id_str(), final_choice.element, final_choice.charge, dxyz,
other_atom.id_str(), other_ion.element, other_ion.charge), file=out)
skipped.append(i_seq)
skip = True
break
if (skip): continue
print(" %s becomes %s%+d" % \
(atom.id_str(), final_choice.element, final_choice.charge), file=out)
refine_adp = params.refine_ion_adp
if (refine_adp == "Auto"):
if (fmodel.f_obs().d_min() <= 1.5):
refine_adp = "anisotropic"
elif (fmodel.f_obs().d_min() < 2.5):
atomic_number = sasaki.table(
final_choice.element).atomic_number()
if (atomic_number >= 19):
refine_adp = "anisotropic"
# Modify the atom object - this is clumsy but they will be grouped into
# a single chain at the end of refinement
initial_b_iso = params.initial_b_iso
if (initial_b_iso is Auto):
initial_b_iso = manager.guess_b_iso_real(i_seq)
element = final_choice.element
if (element == "IOD"): # FIXME
element = "I"
modified_atom = model.convert_atom(
i_seq=i_seq,
scattering_type=final_choice.scattering_type(),
atom_name=element,
element=element,
charge=final_choice.charge,
residue_name=final_choice.element,
initial_occupancy=params.initial_occupancy,
initial_b_iso=initial_b_iso,
chain_id=params.ion_chain_id,
segid="ION",
refine_adp=refine_adp,
refine_occupancies=False) #params.refine_ion_occupancies)
if (params.refine_anomalous) and (anomalous_flag):
scatterer = model.get_xray_structure().scatterers()[i_seq]
if (wavelength is not None):
fp_fdp_info = sasaki.table(
final_choice.element).at_angstrom(wavelength)
scatterer.fp = fp_fdp_info.fp()
scatterer.fdp = fp_fdp_info.fdp()
print(" setting f'=%g, f''=%g" %
(scatterer.fp, scatterer.fdp),
file=out)
group = xray.anomalous_scatterer_group(
iselection=flex.size_t([i_seq]),
f_prime=scatterer.fp,
f_double_prime=scatterer.fdp,
refine=["f_prime", "f_double_prime"],
selection_string=get_single_atom_selection_string(
modified_atom),
update_from_selection=True)
anomalous_groups.append(group)
modified_iselection.append(i_seq)
if (len(modified_iselection) > 0):
scatterers = model.get_xray_structure().scatterers()
# FIXME not sure this is actually working as desired...
site_symmetry_table = model.get_xray_structure().site_symmetry_table()
for i_seq in site_symmetry_table.special_position_indices():
scatterers[i_seq].site = crystal.correct_special_position(
crystal_symmetry=model.get_xray_structure(),
special_op=site_symmetry_table.get(i_seq).special_op(),
site_frac=scatterers[i_seq].site,
site_label=scatterers[i_seq].label,
tolerance=1.0)
model.get_xray_structure().replace_scatterers(scatterers=scatterers)
model.set_xray_structure(model.get_xray_structure())
def show_r_factors():
return "r_work=%6.4f r_free=%6.4f" % (fmodel.r_work(),
fmodel.r_free())
fmodel.update_xray_structure(xray_structure=model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
n_anom = len(anomalous_groups)
refine_anomalous = anomalous_flag and params.refine_anomalous and n_anom > 0
refine_occupancies = (
(params.refine_ion_occupancies or refine_anomalous)
and ((not occupancy_strategy_enabled) or
(model.refinement_flags.s_occupancies is None) or
(len(model.refinement_flags.s_occupancies) == 0)))
if (refine_anomalous):
if (model.have_anomalous_scatterer_groups()
and (group_anomalous_strategy_enabled)):
model.set_anomalous_scatterer_groups(
model.get_anomalous_scatterer_groups() + anomalous_groups)
refine_anomalous = False
if (refine_occupancies) or (refine_anomalous):
print("", file=out)
print(" occupancy refinement (new ions only): start %s" % \
show_r_factors(), file=out)
fmodel.xray_structure.scatterers().flags_set_grads(state=False)
fmodel.xray_structure.scatterers().flags_set_grad_occupancy(
iselection=modified_iselection)
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=25)
minimized = mmtbx.refinement.minimization.lbfgs(
restraints_manager=None,
fmodels=fmodels,
model=model,
is_neutron_scat_table=False,
lbfgs_termination_params=lbfgs_termination_params)
fmodel.xray_structure.adjust_occupancy(
occ_max=1.0, occ_min=0, selection=modified_iselection)
zero_occ = []
for i_seq in modified_iselection:
occ = fmodel.xray_structure.scatterers()[i_seq].occupancy
if (occ == 0):
zero_occ.append(i_seq)
fmodel.update_xray_structure(update_f_calc=True,
update_f_mask=True)
print(" final %s" % \
show_r_factors(), file=out)
if (len(zero_occ) > 0):
print(" WARNING: occupancy dropped to zero for %d atoms:",
file=out)
atoms = model.get_atoms()
for i_seq in zero_occ:
print(" %s" % atoms[i_seq].id_str(suppress_segid=True),
file=out)
print("", file=out)
if (refine_anomalous):
assert fmodel.f_obs().anomalous_flag()
print(" anomalous refinement (new ions only): start %s" % \
show_r_factors(), file=out)
fmodel.update(target_name="ls")
anomalous_scatterer_groups.minimizer(fmodel=fmodel,
groups=anomalous_groups)
fmodel.update(target_name="ml")
print(" final %s" % \
show_r_factors(), file=out)
print("", file=out)
return manager