def exercise_map_utils () :
#
# UNSTABLE
#
hierarchy, fmodel = get_1yjp_pdb_and_fmodel()
sel_cache = hierarchy.atom_selection_cache()
sele = sel_cache.selection("resseq 5 and (name CD or name OE1 or name NE2)")
sele_all = sel_cache.selection("resseq 5")
fmodel.xray_structure.scale_adp(factor=0.5, selection=sele)
fmodel.update_xray_structure(update_f_calc=True)
two_fofc_map, fofc_map = building.get_difference_maps(fmodel)
map_stats = building.local_density_quality(
fofc_map=fofc_map,
two_fofc_map=two_fofc_map,
atom_selection=sele_all,
xray_structure=fmodel.xray_structure)
out = StringIO()
map_stats.show_atoms_outside_density(out=out, two_fofc_cutoff=3.0)
pdb_strs = [ l.split(":")[0] for l in out.getvalue().splitlines() ]
assert len(pdb_strs) > 0
# XXX there seems to be a stochastic effect here
#assert (pdb_strs == ['pdb=" CA GLN A 5 "', 'pdb=" CB GLN A 5 "',
# 'pdb=" CD GLN A 5 "', 'pdb=" NE2 GLN A 5 "']), \
# pdb_strs
fc_map = fmodel.map_coefficients(map_type="Fc").fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map_unpadded()
assert (map_stats.number_of_atoms_below_fofc_map_level() == 3)
assert (map_stats.fraction_of_nearby_grid_points_above_cutoff() > 0.0)
stats = building.get_model_map_stats(
selection=sele_all,
target_map=two_fofc_map,
model_map=fc_map,
unit_cell=fmodel.xray_structure.unit_cell(),
sites_cart=fmodel.xray_structure.sites_cart(),
pdb_atoms=hierarchy.atoms())
def exercise_map_utils () :
#
# UNSTABLE 2x
#
hierarchy, fmodel = get_1yjp_pdb_and_fmodel()
sel_cache = hierarchy.atom_selection_cache()
sele = sel_cache.selection("resseq 5 and (name CD or name OE1 or name NE2)")
sele_all = sel_cache.selection("resseq 5")
fmodel.xray_structure.scale_adp(factor=0.5, selection=sele)
fmodel.update_xray_structure(update_f_calc=True)
two_fofc_map, fofc_map = building.get_difference_maps(fmodel)
map_stats = building.local_density_quality(
fofc_map=fofc_map,
two_fofc_map=two_fofc_map,
atom_selection=sele_all,
xray_structure=fmodel.xray_structure)
out = StringIO()
map_stats.show_atoms_outside_density(out=out, two_fofc_cutoff=3.0)
pdb_strs = [ l.split(":")[0] for l in out.getvalue().splitlines() ]
assert len(pdb_strs) > 0
# XXX there seems to be a stochastic effect here
#assert (pdb_strs == ['pdb=" CA GLN A 5 "', 'pdb=" CB GLN A 5 "',
# 'pdb=" CD GLN A 5 "', 'pdb=" NE2 GLN A 5 "']), \
# pdb_strs
fc_map = fmodel.map_coefficients(map_type="Fc").fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map_unpadded()
assert (map_stats.number_of_atoms_below_fofc_map_level() == 3)
assert (map_stats.fraction_of_nearby_grid_points_above_cutoff() > 0.0)
stats = building.get_model_map_stats(
selection=sele_all,
target_map=two_fofc_map,
model_map=fc_map,
unit_cell=fmodel.xray_structure.unit_cell(),
sites_cart=fmodel.xray_structure.sites_cart(),
pdb_atoms=hierarchy.atoms())
def process_results(pdb_hierarchy,
fmodel,
residues_in,
building_trials,
params,
verbose=False,
log=sys.stdout):
assert (len(residues_in) == len(building_trials))
from mmtbx.rotamer import rotamer_eval
n_alternates = 0
unit_cell = fmodel.xray_structure.unit_cell()
two_fofc_map, fofc_map = building.get_difference_maps(fmodel)
rot_eval = rotamer_eval.RotamerEval(data_version="8000")
for main_conf, trials in zip(residues_in, building_trials):
if (trials is None):
print("WARNING: error building %s" % main_conf.id_str(), file=log)
continue
if (len(trials) == 0):
continue
res_log = StringIO()
print(" %s:" % main_conf.id_str(), file=res_log)
main_rotamer = alt_rotamer = None
if (not main_conf.resname in ["GLY", "PRO", "ALA"]):
main_rotamer = rot_eval.evaluate_residue(main_conf)
assert (main_rotamer != "OUTLIER")
best_trial = pick_best_alternate(trials=trials,
params=params,
rotamer=main_rotamer,
log=res_log)
if (best_trial is None):
continue
new_conf = best_trial.as_atom_group()
changed_rotamer = (best_trial.rotamer != main_rotamer)
skip = False
flag = ""
stats = best_trial.stats
# FIXME this needs to be made more consistent with the filtering criteria
# in disorder/__init__.py
if ((stats.rmsd < params.rmsd_min)
and (stats.max_dev < params.rmsd_min)
and (not changed_rotamer)):
skip = True
print(" selected conformer (occ=%.2f):" % \
best_trial.occupancy, file=res_log)
res_log2 = StringIO()
density_quality = building.residue_density_quality(
atom_group=new_conf,
unit_cell=unit_cell,
two_fofc_map=two_fofc_map,
fofc_map=fofc_map)
if (main_conf.resname in ["CYS", "MET", "MSE"]):
# XXX if we have a heavier atom (S or SE) in the residue, some additional
# sanity checks insure that it has slightly stronger density than we
# require for lighter elements. multipliers are just guesses, taking
# into account rad damage and partial SeMet incorporation.
heavy_atom = {
"CYS": "SG",
"MET": "SD",
"MSE": "SE"
}[main_conf.resname]
mult = {"CYS": 1.6, "MET": 1.6, "MSE": 2.0}[main_conf.resname]
map_levels = density_quality.density_at_atom(heavy_atom)
if (map_levels is None): # this probably shouldn't even happen
skip = True
if ((map_levels.fofc < params.map_thresholds.fofc_min * mult)
or (map_levels.two_fofc <
params.map_thresholds.two_fofc_min * mult)):
skip = True
n_atoms_outside_density = density_quality.show_atoms_outside_density(
two_fofc_cutoff=params.map_thresholds.two_fofc_min,
fofc_cutoff=params.map_thresholds.fofc_min,
out=res_log2,
prefix=" ")
fofc_max = density_quality.max_fofc_value()
if (n_atoms_outside_density > 0):
skip = True
if (not skip) and (verbose):
flag = " ***"
print(" RMSD=%5.3f max. change=%.2f max(Fo-Fc)=%.1f%s" \
% (stats.rmsd, stats.max_dev, fofc_max, flag), file=res_log)
if (changed_rotamer):
print(" starting rotamer=%s new rotamer=%s" % \
(main_rotamer, best_trial.rotamer), file=res_log)
if (n_atoms_outside_density != 0):
print(" atoms outside density:", file=res_log)
print(res_log2.getvalue(), file=res_log)
else:
print("", file=res_log)
if (not skip) or (verbose):
log.write(res_log.getvalue())
if (skip): continue
residue_group = main_conf.parent()
main_conf.altloc = 'A'
new_occ = 0.5
if (params.expected_occupancy is not None):
new_occ = max(0.2, min(0.8, params.expected_occupancy))
for atom in main_conf.atoms():
atom.occ = 1.0 - new_occ
atom.segid = alt_confs.SEGID_MAIN
new_conf = new_conf.detached_copy()
new_conf.altloc = 'B'
for atom in new_conf.atoms():
atom.segid = alt_confs.SEGID_NEW_REBUILT
atom.occ = new_occ
residue_group.append_atom_group(new_conf)
n_alternates += 1
return n_alternates
def filter_before_build (
pdb_hierarchy,
fmodel,
geometry_restraints_manager,
selection=None,
params=None,
verbose=True,
log=sys.stdout) :
"""
Pick residues suitable for building alternate conformations - by default,
this means no MolProbity/geometry outliers, good fit to map, no missing
atoms, and no pre-existing alternates, but with significant difference
density nearby.
"""
from mmtbx.validation import molprobity
from mmtbx.rotamer import rotamer_eval
import mmtbx.monomer_library.server
from mmtbx import building
from iotbx.pdb import common_residue_names_get_class
from scitbx.array_family import flex
if (selection is None) :
selection = flex.bool(fmodel.xray_structure.scatterers().size(), True)
pdb_atoms = pdb_hierarchy.atoms()
assert (pdb_atoms.size() == fmodel.xray_structure.scatterers().size())
pdb_atoms.reset_i_seq()
full_validation = molprobity.molprobity(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=False,
rotamer_library="8000")
if (verbose) :
full_validation.show(out=log)
multi_criterion = full_validation.as_multi_criterion_view()
if (params is None) :
params = libtbx.phil.parse(filter_params_str).extract()
mon_lib_srv = mmtbx.monomer_library.server.server()
two_fofc_map, fofc_map = building.get_difference_maps(fmodel=fmodel)
residues = []
filters = params.discard_outliers
make_sub_header("Identifying candidates for building", out=log)
# TODO parallelize
for chain in pdb_hierarchy.only_model().chains() :
if (not chain.is_protein()) :
continue
for residue_group in chain.residue_groups() :
atom_groups = residue_group.atom_groups()
id_str = residue_group.id_str()
i_seqs = residue_group.atoms().extract_i_seq()
residue_sel = selection.select(i_seqs)
if (not residue_sel.all_eq(True)) :
continue
if (len(atom_groups) > 1) :
print >> log, " %s is already multi-conformer" % id_str
continue
atom_group = atom_groups[0]
res_class = common_residue_names_get_class(atom_group.resname)
if (res_class != "common_amino_acid") :
print >> log, " %s: non-standard residue" % id_str
continue
missing_atoms = rotamer_eval.eval_residue_completeness(
residue=atom_group,
mon_lib_srv=mon_lib_srv,
ignore_hydrogens=True)
if (len(missing_atoms) > 0) :
# residues modeled as pseudo-ALA are allowed by default; partially
# missing sidechains are more problematic
if ((building.is_stub_residue(atom_group)) and
(not params.ignore_stub_residues)) :
pass
else :
print >> log, " %s: missing or incomplete sidechain" % \
(id_str, len(missing_atoms))
continue
validation = multi_criterion.get_residue_group_data(residue_group)
is_outlier = is_validation_outlier(validation, params)
if (is_outlier) :
print >> log, " %s" % str(validation)
continue
if (params.use_difference_map) :
i_seqs_no_hd = building.get_non_hydrogen_atom_indices(residue_group)
map_stats = building.local_density_quality(
fofc_map=fofc_map,
two_fofc_map=two_fofc_map,
atom_selection=i_seqs_no_hd,
xray_structure=fmodel.xray_structure,
radius=params.sampling_radius)
if ((map_stats.number_of_atoms_below_fofc_map_level() == 0) and
(map_stats.fraction_of_nearby_grid_points_above_cutoff()==0)) :
if (verbose) :
print >> log, " no difference density for %s" % id_str
continue
residues.append(residue_group.only_atom_group())
if (len(residues) == 0) :
raise Sorry("No residues passed the filtering criteria.")
print >> log, ""
print >> log, "Alternate conformations will be tried for %d residue(s):" % \
len(residues)
building.show_chain_resseq_ranges(residues, out=log, prefix=" ")
print >> log, ""
return residues
def process_results (
pdb_hierarchy,
fmodel,
residues_in,
building_trials,
params,
verbose=False,
log=sys.stdout) :
assert (len(residues_in) == len(building_trials))
from mmtbx.rotamer import rotamer_eval
n_alternates = 0
unit_cell = fmodel.xray_structure.unit_cell()
two_fofc_map, fofc_map = building.get_difference_maps(fmodel)
rot_eval = rotamer_eval.RotamerEval(data_version="8000")
for main_conf, trials in zip(residues_in, building_trials) :
if (trials is None) :
print >> log, "WARNING: error building %s" % main_conf.id_str()
continue
if (len(trials) == 0) :
continue
res_log = StringIO()
print >> res_log, " %s:" % main_conf.id_str()
main_rotamer = alt_rotamer = None
if (not main_conf.resname in ["GLY","PRO","ALA"]) :
main_rotamer = rot_eval.evaluate_residue(main_conf)
assert (main_rotamer != "OUTLIER")
best_trial = pick_best_alternate(
trials=trials,
params=params,
rotamer=main_rotamer,
log=res_log)
if (best_trial is None) :
continue
new_conf = best_trial.as_atom_group()
changed_rotamer = (best_trial.rotamer != main_rotamer)
skip = False
flag = ""
stats = best_trial.stats
# FIXME this needs to be made more consistent with the filtering criteria
# in disorder/__init__.py
if ((stats.rmsd < params.rmsd_min) and
(stats.max_dev < params.rmsd_min) and
(not changed_rotamer)) :
skip = True
print >> res_log, " selected conformer (occ=%.2f):" % \
best_trial.occupancy
res_log2 = StringIO()
density_quality = building.residue_density_quality(
atom_group=new_conf,
unit_cell=unit_cell,
two_fofc_map=two_fofc_map,
fofc_map=fofc_map)
if (main_conf.resname in ["CYS", "MET", "MSE"]) :
# XXX if we have a heavier atom (S or SE) in the residue, some additional
# sanity checks insure that it has slightly stronger density than we
# require for lighter elements. multipliers are just guesses, taking
# into account rad damage and partial SeMet incorporation.
heavy_atom = {"CYS":"SG", "MET":"SD", "MSE":"SE"}[main_conf.resname]
mult = {"CYS":1.6, "MET":1.6, "MSE":2.0}[main_conf.resname]
map_levels = density_quality.density_at_atom(heavy_atom)
if (map_levels is None) : # this probably shouldn't even happen
skip = True
if ((map_levels.fofc < params.map_thresholds.fofc_min*mult) or
(map_levels.two_fofc < params.map_thresholds.two_fofc_min*mult)) :
skip = True
n_atoms_outside_density = density_quality.show_atoms_outside_density(
two_fofc_cutoff=params.map_thresholds.two_fofc_min,
fofc_cutoff=params.map_thresholds.fofc_min,
out=res_log2,
prefix=" ")
fofc_max = density_quality.max_fofc_value()
if (n_atoms_outside_density > 0) :
skip = True
if (not skip) and (verbose) :
flag = " ***"
print >> res_log, \
" RMSD=%5.3f max. change=%.2f max(Fo-Fc)=%.1f%s" \
% (stats.rmsd, stats.max_dev, fofc_max, flag)
if (changed_rotamer) :
print >> res_log, " starting rotamer=%s new rotamer=%s" % \
(main_rotamer, best_trial.rotamer)
if (n_atoms_outside_density != 0) :
print >> res_log, " atoms outside density:"
print >> res_log, res_log2.getvalue()
else :
print >> res_log, ""
if (not skip) or (verbose) :
log.write(res_log.getvalue())
if (skip) : continue
residue_group = main_conf.parent()
main_conf.altloc = 'A'
new_occ = 0.5
if (params.expected_occupancy is not None) :
new_occ = max(0.2, min(0.8, params.expected_occupancy))
for atom in main_conf.atoms() :
atom.occ = 1.0 - new_occ
atom.segid = alt_confs.SEGID_MAIN
new_conf = new_conf.detached_copy()
new_conf.altloc = 'B'
for atom in new_conf.atoms() :
atom.segid = alt_confs.SEGID_NEW_REBUILT
atom.occ = new_occ
residue_group.append_atom_group(new_conf)
n_alternates += 1
return n_alternates
