def run(prefix="tst_00"):
# Good answer model
pdb_file_name_answer = "%s_answer.pdb" % prefix
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_answer)
pdb_inp.write_pdb_file(file_name="%s_answer.pdb" % prefix)
ph_answer = pdb_inp.construct_hierarchy()
ph_answer.atoms().reset_i_seq()
xrs_answer = pdb_inp.xray_structure_simple()
# Poor model that we want to refine so it matches the answer
pdb_file_name_poor = "%s_poor.pdb" % prefix
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_poor)
pdb_inp.write_pdb_file(file_name="%s_poor.pdb" % prefix)
ph_poor = pdb_inp.construct_hierarchy()
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp.xray_structure_simple()
# Initialize states accumulator
states = mmtbx.utils.states(pdb_hierarchy=ph_answer, xray_structure=xrs_poor)
states.add(sites_cart=xrs_poor.sites_cart())
# Compute target map
fc = xrs_answer.structure_factors(d_min=3.5).f_calc()
fft_map = fc.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
target_map_data = fft_map.real_map_unpadded()
ccp4_map(crystal_symmetry=fc.crystal_symmetry(), file_name="map.ccp4", map_data=target_map_data)
# Output map coefficients
mtz_dataset = fc.as_mtz_dataset(column_root_label="FC")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name="map.mtz")
# Build geometry restraints
params = monomer_library.pdb_interpretation.master_params.extract()
# params.nonbonded_weight=200
# params.peptide_link.ramachandran_restraints=True
# params.peptide_link.rama_potential="emsley"
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=monomer_library.server.server(),
ener_lib=monomer_library.server.ener_lib(),
raw_records=pdb_str_poor,
params=params,
strict_conflict_handling=True,
force_symmetry=True,
log=None,
)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False, plain_pairs_radius=5, assume_hydrogens_all_missing=True
)
restraints_manager = mmtbx.restraints.manager(geometry=geometry, normalization=True)
# Do real-space refinement
t0 = time.time()
ear = mmtbx.refinement.real_space.explode_and_refine.run(
xray_structure=xrs_poor,
pdb_hierarchy=ph_poor,
map_data=target_map_data,
restraints_manager=restraints_manager,
states=states,
nproc=1,
)
print "Time: %6.4f" % (time.time() - t0)
ear.pdb_hierarchy.write_pdb_file(file_name="%s_refined.pdb" % prefix)
states.write(file_name="%s_refined_all_states.pdb" % prefix)
def write_output_files(self, mtz_file_name, ccp4_map_file_name, fem_label,
orig_label):
mtz_dataset = self.mc_result.as_mtz_dataset(column_root_label=fem_label)
mtz_dataset.add_miller_array(
miller_array = self.mc_orig,
column_root_label = orig_label)
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name = mtz_file_name)
ccp4_map(cg=self.crystal_gridding, file_name=ccp4_map_file_name,
map_data=self.map_result)
def run(prefix="tst_00"):
# Poor model that we want to refine so it matches the answer
pdb_inp = iotbx.pdb.input(file_name="poor_model.pdb")
ph_poor = pdb_inp.construct_hierarchy()
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp.xray_structure_simple()
# Initialize states accumulator
states = mmtbx.utils.states(pdb_hierarchy=ph_poor, xray_structure=xrs_poor)
states.add(sites_cart=xrs_poor.sites_cart())
# Compute target map
mas = reflection_file_reader.any_reflection_file(
file_name="poor_map.mtz").as_miller_arrays()
assert len(mas) == 1
fc = mas[0]
fft_map = fc.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
target_map_data = fft_map.real_map_unpadded()
ccp4_map(crystal_symmetry=fc.crystal_symmetry(),
file_name="map.ccp4",
map_data=target_map_data)
# Build geometry restraints
params = monomer_library.pdb_interpretation.master_params.extract()
params.nonbonded_weight = 200
#params.peptide_link.ramachandran_restraints=True
#params.peptide_link.rama_potential="oldfield"
#print dir(params)
#STOP()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=monomer_library.server.server(),
ener_lib=monomer_library.server.ener_lib(),
file_name="poor_model.pdb",
params=params,
#crystal_symmetry = fc.crystal_symmetry(),
strict_conflict_handling=True,
force_symmetry=True,
log=None)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False,
plain_pairs_radius=5,
assume_hydrogens_all_missing=True)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
#for a in ph_answer.atoms():
# print a.i_seq, a.name, a.xyz
#STOP()
#ref_xyz = flex.vec3_double([(14.323, 35.055, 14.635), (16.099, 12.317, 16.37)])
#selection = flex.size_t([1,76])
#
#restraints_manager.geometry.adopt_reference_coordinate_restraints_in_place(
# reference.add_coordinate_restraints(
# sites_cart = ref_xyz,
# selection = selection,
# sigma = 0.1))
# Do real-space refinement
t0 = time.time()
ear = mmtbx.refinement.real_space.explode_and_refine.run(
xray_structure=xrs_poor,
pdb_hierarchy=ph_poor,
map_data=target_map_data,
restraints_manager=restraints_manager,
states=states)
print "Time: %6.4f" % (time.time() - t0)
ear.pdb_hierarchy.write_pdb_file(file_name="%s_refined.pdb" % prefix)
states.write(file_name="%s_refined_all_states.pdb" % prefix)
def run(prefix="tst_00"):
# Poor model that we want to refine so it matches the answer
pdb_inp = iotbx.pdb.input(file_name="poor_model.pdb")
ph_poor = pdb_inp.construct_hierarchy()
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp.xray_structure_simple()
# Initialize states accumulator
states = mmtbx.utils.states(pdb_hierarchy=ph_poor, xray_structure=xrs_poor)
states.add(sites_cart = xrs_poor.sites_cart())
# Compute target map
mas = reflection_file_reader.any_reflection_file(file_name =
"poor_map.mtz").as_miller_arrays()
assert len(mas)==1
fc = mas[0]
fft_map = fc.fft_map(resolution_factor = 0.25)
fft_map.apply_sigma_scaling()
target_map_data = fft_map.real_map_unpadded()
ccp4_map(crystal_symmetry=fc.crystal_symmetry(), file_name="map.ccp4",
map_data=target_map_data)
# Build geometry restraints
params = monomer_library.pdb_interpretation.master_params.extract()
params.nonbonded_weight=200
#params.peptide_link.ramachandran_restraints=True
#params.peptide_link.rama_potential="oldfield"
#print dir(params)
#STOP()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv = monomer_library.server.server(),
ener_lib = monomer_library.server.ener_lib(),
file_name = "poor_model.pdb",
params = params,
#crystal_symmetry = fc.crystal_symmetry(),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies = False,
plain_pairs_radius = 5,
assume_hydrogens_all_missing = True)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry,
normalization = True)
#for a in ph_answer.atoms():
# print a.i_seq, a.name, a.xyz
#STOP()
#ref_xyz = flex.vec3_double([(14.323, 35.055, 14.635), (16.099, 12.317, 16.37)])
#selection = flex.size_t([1,76])
#
#restraints_manager.geometry.adopt_reference_coordinate_restraints_in_place(
# reference.add_coordinate_restraints(
# sites_cart = ref_xyz,
# selection = selection,
# sigma = 0.1))
# Do real-space refinement
t0=time.time()
ear = mmtbx.refinement.real_space.explode_and_refine.run(
xray_structure = xrs_poor,
pdb_hierarchy = ph_poor,
map_data = target_map_data,
restraints_manager = restraints_manager,
states = states)
print "Time: %6.4f"%(time.time()-t0)
ear.pdb_hierarchy.write_pdb_file(file_name="%s_refined.pdb"%prefix)
states.write(file_name="%s_refined_all_states.pdb"%prefix)
def run(prefix="tst_00"):
# Good answer model
pdb_file_name_answer = "%s_answer.pdb" % prefix
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_answer)
pdb_inp.write_pdb_file(file_name="%s_answer.pdb" % prefix)
ph_answer = pdb_inp.construct_hierarchy()
ph_answer.atoms().reset_i_seq()
xrs_answer = pdb_inp.xray_structure_simple()
# Poor model that we want to refine so it matches the answer
pdb_file_name_poor = "%s_poor.pdb" % prefix
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_poor)
pdb_inp.write_pdb_file(file_name="%s_poor.pdb" % prefix)
ph_poor = pdb_inp.construct_hierarchy()
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp.xray_structure_simple()
# Initialize states accumulator
states = mmtbx.utils.states(pdb_hierarchy=ph_answer,
xray_structure=xrs_poor)
states.add(sites_cart=xrs_poor.sites_cart())
# Compute target map
fc = xrs_answer.structure_factors(d_min=3.5).f_calc()
fft_map = fc.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
target_map_data = fft_map.real_map_unpadded()
ccp4_map(crystal_symmetry=fc.crystal_symmetry(),
file_name="map.ccp4",
map_data=target_map_data)
# Output map coefficients
mtz_dataset = fc.as_mtz_dataset(column_root_label="FC")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name="map.mtz")
# Build geometry restraints
params = monomer_library.pdb_interpretation.master_params.extract()
#params.nonbonded_weight=200
#params.peptide_link.ramachandran_restraints=True
#params.peptide_link.rama_potential="emsley"
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=monomer_library.server.server(),
ener_lib=monomer_library.server.ener_lib(),
raw_records=pdb_str_poor,
params=params,
strict_conflict_handling=True,
force_symmetry=True,
log=None)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False,
plain_pairs_radius=5,
assume_hydrogens_all_missing=True)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
# Do real-space refinement
t0 = time.time()
ear = mmtbx.refinement.real_space.explode_and_refine.run(
xray_structure=xrs_poor,
pdb_hierarchy=ph_poor,
map_data=target_map_data,
restraints_manager=restraints_manager,
states=states,
nproc=1)
print "Time: %6.4f" % (time.time() - t0)
ear.pdb_hierarchy.write_pdb_file(file_name="%s_refined.pdb" % prefix)
states.write(file_name="%s_refined_all_states.pdb" % prefix)