def from_pdb(self):
out = self.out
params = self.params
pdb_hierarchy = self.pdb_hierarchy
pdb_sg, pdb_uc = None, None
pdb_symm = self.pdb_in.crystal_symmetry()
if (pdb_symm is not None):
pdb_sg = pdb_symm.space_group_info()
pdb_uc = pdb_symm.unit_cell()
apply_sg = pdb_sg
apply_uc = pdb_uc
if (params.crystal_symmetry.space_group is not None):
apply_sg = params.crystal_symmetry.space_group
else:
params.crystal_symmetry.space_group = pdb_sg
if (params.crystal_symmetry.unit_cell is not None):
apply_uc = params.crystal_symmetry.unit_cell
else:
params.crystal_symmetry.unit_cell = pdb_uc
if (apply_sg is None) or (apply_uc is None):
raise Sorry(
"Incomplete symmetry information - please specify a space " +
"group and unit cell for this structure.")
from cctbx import crystal, adptbx
from scitbx.array_family import flex
apply_symm = crystal.symmetry(unit_cell=apply_uc,
space_group_info=apply_sg)
if (params.modify_pdb.remove_waters):
print(" Removing solvent atoms...", file=out)
for model in pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups():
if (atom_group.resname in ["HOH", "WAT"]):
residue_group.remove_atom_group(
atom_group=atom_group)
if (len(residue_group.atom_groups()) == 0):
chain.remove_residue_group(
residue_group=residue_group)
if (len(chain.atoms()) == 0):
model.remove_chain(chain=chain)
if (params.modify_pdb.remove_alt_confs):
print(
" Removing all alternate conformations and resetting occupancies...",
file=out)
from mmtbx import pdbtools
pdbtools.remove_alt_confs(hierarchy=pdb_hierarchy)
xray_structure = self.pdb_in.xray_structure_simple(
crystal_symmetry=apply_symm)
sctr_keys = xray_structure.scattering_type_registry().type_count_dict()
hd_selection = xray_structure.hd_selection()
if (not (("H" in sctr_keys) or ("D" in sctr_keys))):
print(" WARNING: this model does not contain hydrogen atoms!",
file=out)
print(" strongly recommend running phenix.ready_set or",
file=out)
print(" equivalent to ensure realistic simulated data.",
file=out)
print("", file=out)
if (params.modify_pdb.convert_to_isotropic):
xray_structure.convert_to_isotropic()
set_b = None
if (params.modify_pdb.set_mean_b_iso is not None):
assert (not params.modify_pdb.set_wilson_b)
print(" Scaling B-factors to have mean of %.2f" % \
params.modify_pdb.set_mean_b_iso, file=out)
assert (params.modify_pdb.set_mean_b_iso > 0)
set_b = params.modify_pdb.set_mean_b_iso
elif (params.modify_pdb.set_wilson_b):
print(
" Scaling B-factors to match mean Wilson B for this resolution",
file=out)
set_b = get_mean_statistic_for_resolution(d_min=params.d_min,
stat_type="wilson_b")
print("", file=out)
if (set_b is not None):
u_iso = xray_structure.extract_u_iso_or_u_equiv()
u_iso = u_iso.select(~hd_selection)
u_mean = flex.mean(u_iso)
b_mean = adptbx.u_as_b(u_mean)
scale = set_b / b_mean
xray_structure.scale_adps(scale)
pdb_hierarchy.atoms().set_adps_from_scatterers(
scatterers=xray_structure.scatterers(),
unit_cell=xray_structure.unit_cell())
import mmtbx.command_line.fmodel
from mmtbx import utils
fmodel_params = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params.extract(
)
fmodel_params.high_resolution = params.d_min
fake_data = params.fake_data_from_fmodel
fmodel_params.fmodel = fake_data.fmodel
if (fmodel_params.fmodel.b_sol == 0):
print(" b_sol is zero - will use mean value for d_min +/- 0.2A",
file=out)
print(" (this is not strongly correlated with resolution, but",
file=out)
print(
" it is preferrable to use a real value instead of leaving",
file=out)
print(" it set to 0)", file=out)
fmodel_params.fmodel.b_sol = 46.0
print("", file=out)
if (fmodel_params.fmodel.k_sol == 0):
print(" k_sol is zero - will use mean value for d_min +/- 0.2A",
file=out)
print(" (this is not strongly correlated with resolution, but",
file=out)
print(
" it is preferrable to use a real value instead of leaving",
file=out)
print(" it set to 0)", file=out)
fmodel_params.fmodel.k_sol = 0.35
print("", file=out)
fmodel_params.structure_factors_accuracy = fake_data.structure_factors_accuracy
fmodel_params.mask = fake_data.mask
fmodel_params.r_free_flags_fraction = params.r_free_flags.fraction
fmodel_params.add_sigmas = False
fmodel_params.output.type = "real"
fmodel_ = utils.fmodel_from_xray_structure(
xray_structure=xray_structure, params=fmodel_params)
f_model = fmodel_.f_model
r_free_flags = fmodel_.r_free_flags
return (f_model, r_free_flags)
def from_pdb (self) :
out = self.out
params = self.params
pdb_hierarchy = self.pdb_hierarchy
pdb_sg, pdb_uc = None, None
pdb_symm = self.pdb_in.crystal_symmetry()
if (pdb_symm is not None) :
pdb_sg = pdb_symm.space_group_info()
pdb_uc = pdb_symm.unit_cell()
apply_sg = pdb_sg
apply_uc = pdb_uc
if (params.crystal_symmetry.space_group is not None) :
apply_sg = params.crystal_symmetry.space_group
else :
params.crystal_symmetry.space_group = pdb_sg
if (params.crystal_symmetry.unit_cell is not None) :
apply_uc = params.crystal_symmetry.unit_cell
else :
params.crystal_symmetry.unit_cell = pdb_uc
if (apply_sg is None) or (apply_uc is None) :
raise Sorry("Incomplete symmetry information - please specify a space "+
"group and unit cell for this structure.")
from cctbx import crystal, adptbx
from scitbx.array_family import flex
apply_symm = crystal.symmetry(
unit_cell=apply_uc,
space_group_info=apply_sg)
if (params.modify_pdb.remove_waters) :
print >> out, " Removing solvent atoms..."
for model in pdb_hierarchy.models() :
for chain in model.chains() :
for residue_group in chain.residue_groups() :
for atom_group in residue_group.atom_groups() :
if (atom_group.resname in ["HOH", "WAT"]) :
residue_group.remove_atom_group(atom_group=atom_group)
if (len(residue_group.atom_groups()) == 0) :
chain.remove_residue_group(residue_group=residue_group)
if (len(chain.atoms()) == 0) :
model.remove_chain(chain=chain)
if (params.modify_pdb.remove_alt_confs) :
print >> out, " Removing all alternate conformations and resetting occupancies..."
from mmtbx import pdbtools
pdbtools.remove_alt_confs(hierarchy=pdb_hierarchy)
xray_structure = self.pdb_in.xray_structure_simple(
crystal_symmetry=apply_symm)
sctr_keys = xray_structure.scattering_type_registry().type_count_dict().keys()
hd_selection = xray_structure.hd_selection()
if (not (("H" in sctr_keys) or ("D" in sctr_keys))) :
print >> out, " WARNING: this model does not contain hydrogen atoms!"
print >> out, " strongly recommend running phenix.ready_set or"
print >> out, " equivalent to ensure realistic simulated data."
print >> out, ""
if (params.modify_pdb.convert_to_isotropic) :
xray_structure.convert_to_isotropic()
set_b = None
if (params.modify_pdb.set_mean_b_iso is not None) :
assert (not params.modify_pdb.set_wilson_b)
print >> out, " Scaling B-factors to have mean of %.2f" % \
params.modify_pdb.set_mean_b_iso
assert (params.modify_pdb.set_mean_b_iso > 0)
set_b = params.modify_pdb.set_mean_b_iso
elif (params.modify_pdb.set_wilson_b) :
print >> out, " Scaling B-factors to match mean Wilson B for this resolution"
set_b = get_mean_statistic_for_resolution(
d_min=params.d_min,
stat_type="wilson_b")
print >> out, ""
if (set_b is not None) :
u_iso = xray_structure.extract_u_iso_or_u_equiv()
u_iso = u_iso.select(~hd_selection)
u_mean = flex.mean(u_iso)
b_mean = adptbx.u_as_b(u_mean)
scale = set_b / b_mean
xray_structure.scale_adps(scale)
pdb_hierarchy.atoms().set_adps_from_scatterers(
scatterers=xray_structure.scatterers(),
unit_cell=xray_structure.unit_cell())
import mmtbx.command_line.fmodel
from mmtbx import utils
fmodel_params = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params.extract()
fmodel_params.high_resolution = params.d_min
fake_data = params.fake_data_from_fmodel
fmodel_params.fmodel = fake_data.fmodel
if (fmodel_params.fmodel.b_sol == 0) :
print >> out, " b_sol is zero - will use mean value for d_min +/- 0.2A"
print >> out, " (this is not strongly correlated with resolution, but"
print >> out, " it is preferrable to use a real value instead of leaving"
print >> out, " it set to 0)"
fmodel_params.fmodel.b_sol = 46.0
print >> out, ""
if (fmodel_params.fmodel.k_sol == 0) :
print >> out, " k_sol is zero - will use mean value for d_min +/- 0.2A"
print >> out, " (this is not strongly correlated with resolution, but"
print >> out, " it is preferrable to use a real value instead of leaving"
print >> out, " it set to 0)"
fmodel_params.fmodel.k_sol = 0.35
print >> out, ""
fmodel_params.structure_factors_accuracy = fake_data.structure_factors_accuracy
fmodel_params.mask = fake_data.mask
fmodel_params.r_free_flags_fraction = params.r_free_flags.fraction
fmodel_params.add_sigmas = False
fmodel_params.output.type = "real"
fmodel_ = utils.fmodel_from_xray_structure(
xray_structure=xray_structure,
params=fmodel_params)
f_model = fmodel_.f_model
r_free_flags = fmodel_.r_free_flags
return (f_model, r_free_flags)
def strip_model(pdb_hierarchy=None,
xray_structure=None,
file_name=None,
params=None,
remove_waters=True,
remove_hydrogens=True,
remove_alt_confs=True,
convert_semet_to_met=True,
convert_to_isotropic=True,
reset_occupancies=True,
remove_ligands=False,
reset_hetatm_flag=False,
preserve_remarks=False,
preserve_symmetry=True,
add_remarks=None,
output_file=None,
log=None):
"""
Utility for removing extraneous records from a model intended for use in
molecular replacement, etc., including waters, alternate conformations,
and other features specific to a particular dataset.
"""
if (params is not None):
remove_waters = params.remove_waters
remove_hydrogens = params.remove_hydrogens
remove_alt_confs = params.remove_alt_confs
convert_semet_to_met = params.convert_semet_to_met
convert_to_isotropic = params.convert_to_isotropic
reset_occupancies = params.reset_occupancies
remove_ligands = params.remove_ligands
reset_hetatm_flag = params.reset_hetatm_flag
if (log is None):
log = null_out()
make_sub_header("Processing input model", out=log)
from mmtbx import pdbtools
remarks = None
if (file_name is not None):
print >> log, "Reading model from %s" % file_name
assert ([pdb_hierarchy, xray_structure] == [None, None])
from iotbx import file_reader
pdb_in = file_reader.any_file(file_name,
force_type="pdb",
raise_sorry_if_errors=True)
pdb_in.check_file_type("pdb")
remarks = pdb_in.file_object.input.remark_section()
pdb_hierarchy = pdb_in.file_object.hierarchy
xray_structure = pdb_in.file_object.xray_structure_simple()
else:
# XXX work with copies, not the original structure
pdb_hierarchy = pdb_hierarchy.deep_copy()
xray_structure = xray_structure.deep_copy_scatterers()
pdb_hierarchy.atoms().reset_i_seq()
if (len(pdb_hierarchy.models()) > 1):
raise Sorry("Multiple models not supported.")
if (remove_hydrogens):
sele = ~(xray_structure.hd_selection())
n_hd = sele.count(False)
if (n_hd > 0):
pdb_hierarchy = pdb_hierarchy.select(sele)
xray_structure = xray_structure.select(sele)
print >> log, " removed %d hydrogens" % n_hd
pdb_hierarchy.atoms().reset_i_seq()
if (remove_waters):
sele = pdb_hierarchy.atom_selection_cache().selection(
"not (resname HOH)")
n_wat = sele.count(False)
if (n_wat > 0):
pdb_hierarchy = pdb_hierarchy.select(sele)
xray_structure = xray_structure.select(sele)
print >> log, " removed %d waters" % n_wat
pdb_hierarchy.atoms().reset_i_seq()
assert_identical_id_str = True
if (remove_alt_confs):
n_atoms_start = xray_structure.scatterers().size()
pdbtools.remove_alt_confs(pdb_hierarchy)
i_seqs = pdb_hierarchy.atoms().extract_i_seq()
n_atoms_end = i_seqs.size()
if (n_atoms_end != n_atoms_start):
print >> log, " removed %d atoms in alternate conformations" % \
(n_atoms_end - n_atoms_start)
assert_identical_id_str = False
xray_structure = xray_structure.select(i_seqs)
pdb_hierarchy.atoms().reset_i_seq()
if (convert_semet_to_met):
# XXX need to start from a copy here because the atom-parent relationship
# seems to be messed up otherwise. this is probably a bug.
pdb_hierarchy = pdb_hierarchy.deep_copy()
n_mse = pdbtools.convert_semet_to_met(pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure)
if (n_mse > 0):
print >> log, " removed %d selenomethionine (MSE) residues" % n_mse
assert_identical_id_str = False
open("tmp1.pdb", "w").write(pdb_hierarchy.as_pdb_string())
sel = pdb_hierarchy.atom_selection_cache().selection
assert sel("resname MSE").count(True) == 0
if (convert_to_isotropic):
xray_structure.convert_to_isotropic()
pdb_hierarchy.adopt_xray_structure(
xray_structure, assert_identical_id_str=assert_identical_id_str)
print >> log, " converted all atoms to isotropic B-factors"
if (reset_occupancies):
assert (remove_alt_confs)
xray_structure.adjust_occupancy(occ_max=1.0, occ_min=1.0)
pdb_hierarchy.adopt_xray_structure(
xray_structure, assert_identical_id_str=assert_identical_id_str)
print >> log, " reset occupancy to 1.0 for all atoms"
if (reset_hetatm_flag):
for atom in pdb_hierarchy.atoms():
atom.hetero = False
if (remove_ligands):
pdb_hierarchy.atoms().reset_i_seq()
model = pdb_hierarchy.only_model()
for chain in model.chains():
if (not chain.is_protein()) and (not chain.is_na()):
print >> log, " removing %d ligand atoms in chain '%s'" % \
(len(chain.atoms()), chain.id)
model.remove_chain(chain)
i_seqs = pdb_hierarchy.atoms().extract_i_seq()
xray_structure = xray_structure.select(i_seqs)
pdb_hierarchy.atoms().reset_i_seq()
assert xray_structure.scatterers().size() == pdb_hierarchy.atoms_size()
if (output_file is not None):
f = open(output_file, "w")
if (add_remarks is not None):
f.write("\n".join(add_remarks))
f.write("\n")
if (preserve_remarks) and (remarks is not None):
f.write("\n".join(remarks))
f.write("\n")
symm = None
if (preserve_symmetry):
symm = xray_structure
f.write(pdb_hierarchy.as_pdb_string(crystal_symmetry=symm))
f.close()
print >> log, " wrote model to %s" % output_file
return pdb_hierarchy, xray_structure
def strip_model (
pdb_hierarchy=None,
xray_structure=None,
file_name=None,
params=None,
remove_waters=True,
remove_hydrogens=True,
remove_alt_confs=True,
convert_semet_to_met=True,
convert_to_isotropic=True,
reset_occupancies=True,
remove_ligands=False,
reset_hetatm_flag=False,
preserve_remarks=False,
preserve_symmetry=True,
add_remarks=None,
output_file=None,
log=None) :
"""
Utility for removing extraneous records from a model intended for use in
molecular replacement, etc., including waters, alternate conformations,
and other features specific to a particular dataset.
"""
if (params is not None) :
remove_waters = params.remove_waters
remove_hydrogens = params.remove_hydrogens
remove_alt_confs = params.remove_alt_confs
convert_semet_to_met = params.convert_semet_to_met
convert_to_isotropic = params.convert_to_isotropic
reset_occupancies = params.reset_occupancies
remove_ligands = params.remove_ligands
reset_hetatm_flag = params.reset_hetatm_flag
if (log is None) :
log = null_out()
make_sub_header("Processing input model", out=log)
from mmtbx import pdbtools
remarks = None
if (file_name is not None) :
print >> log, "Reading model from %s" % file_name
assert ([pdb_hierarchy, xray_structure] == [None, None])
from iotbx import file_reader
pdb_in = file_reader.any_file(file_name, force_type="pdb",
raise_sorry_if_errors=True)
pdb_in.check_file_type("pdb")
remarks = pdb_in.file_object.input.remark_section()
pdb_hierarchy = pdb_in.file_object.hierarchy
xray_structure = pdb_in.file_object.xray_structure_simple()
else :
# XXX work with copies, not the original structure
pdb_hierarchy = pdb_hierarchy.deep_copy()
xray_structure = xray_structure.deep_copy_scatterers()
pdb_hierarchy.atoms().reset_i_seq()
if (len(pdb_hierarchy.models()) > 1) :
raise Sorry("Multiple models not supported.")
if (remove_hydrogens) :
sele = ~(xray_structure.hd_selection())
n_hd = sele.count(False)
if (n_hd > 0) :
pdb_hierarchy = pdb_hierarchy.select(sele)
xray_structure = xray_structure.select(sele)
print >> log, " removed %d hydrogens" % n_hd
pdb_hierarchy.atoms().reset_i_seq()
if (remove_waters) :
sele = pdb_hierarchy.atom_selection_cache().selection("not (resname HOH)")
n_wat = sele.count(False)
if (n_wat > 0) :
pdb_hierarchy = pdb_hierarchy.select(sele)
xray_structure = xray_structure.select(sele)
print >> log, " removed %d waters" % n_wat
pdb_hierarchy.atoms().reset_i_seq()
assert_identical_id_str = True
if (remove_alt_confs) :
n_atoms_start = xray_structure.scatterers().size()
pdbtools.remove_alt_confs(pdb_hierarchy)
i_seqs = pdb_hierarchy.atoms().extract_i_seq()
n_atoms_end = i_seqs.size()
if (n_atoms_end != n_atoms_start) :
print >> log, " removed %d atoms in alternate conformations" % \
(n_atoms_end - n_atoms_start)
assert_identical_id_str = False
xray_structure = xray_structure.select(i_seqs)
pdb_hierarchy.atoms().reset_i_seq()
if (convert_semet_to_met) :
# XXX need to start from a copy here because the atom-parent relationship
# seems to be messed up otherwise. this is probably a bug.
pdb_hierarchy = pdb_hierarchy.deep_copy()
n_mse = pdbtools.convert_semet_to_met(
pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure)
if (n_mse > 0) :
print >> log, " removed %d selenomethionine (MSE) residues" % n_mse
assert_identical_id_str = False
open("tmp1.pdb", "w").write(pdb_hierarchy.as_pdb_string())
sel = pdb_hierarchy.atom_selection_cache().selection
assert sel("resname MSE").count(True) == 0
if (convert_to_isotropic) :
xray_structure.convert_to_isotropic()
pdb_hierarchy.adopt_xray_structure(xray_structure,
assert_identical_id_str=assert_identical_id_str)
print >> log, " converted all atoms to isotropic B-factors"
if (reset_occupancies) :
assert (remove_alt_confs)
xray_structure.adjust_occupancy(occ_max=1.0, occ_min=1.0)
pdb_hierarchy.adopt_xray_structure(xray_structure,
assert_identical_id_str=assert_identical_id_str)
print >> log, " reset occupancy to 1.0 for all atoms"
if (reset_hetatm_flag) :
for atom in pdb_hierarchy.atoms() :
atom.hetero = False
if (remove_ligands) :
pdb_hierarchy.atoms().reset_i_seq()
model = pdb_hierarchy.only_model()
for chain in model.chains() :
if (not chain.is_protein()) and (not chain.is_na()) :
print >> log, " removing %d ligand atoms in chain '%s'" % \
(len(chain.atoms()), chain.id)
model.remove_chain(chain)
i_seqs = pdb_hierarchy.atoms().extract_i_seq()
xray_structure = xray_structure.select(i_seqs)
pdb_hierarchy.atoms().reset_i_seq()
assert xray_structure.scatterers().size() == pdb_hierarchy.atoms_size()
if (output_file is not None) :
f = open(output_file, "w")
if (add_remarks is not None) :
f.write("\n".join(add_remarks))
f.write("\n")
if (preserve_remarks) and (remarks is not None) :
f.write("\n".join(remarks))
f.write("\n")
symm = None
if (preserve_symmetry) :
symm = xray_structure
f.write(pdb_hierarchy.as_pdb_string(crystal_symmetry=symm))
f.close()
print >> log, " wrote model to %s" % output_file
return pdb_hierarchy, xray_structure
