def exercise():
import mmtbx.utils
from iotbx.file_reader import any_file
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/CypA_refine_3.pdb",
test=os.path.isfile)
mtz_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/3k0n.mtz",
test=os.path.isfile)
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.construct_hierarchy()
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0].f_sq_as_f()
flags = mtz_in.file_server.miller_arrays[-1]
flags = flags.customized_copy(data=(flags.data() == 0))
assert ((flags.data().count(True) / len(flags.data())) <= 0.1)
f_obs, flags = f_obs.common_sets(other=flags)
fmodel = mmtbx.utils.fmodel_simple(f_obs=f_obs,
r_free_flags=flags,
scattering_table="n_gaussian",
xray_structures=[xrs])
fmodel.info().show_targets()
selection = hierarchy.atom_selection_cache().selection(
"chain A and resseq 111:115")
two_fofc_map, fofc_map, = disorder.get_partial_omit_map(
fmodel=fmodel,
selection=selection,
map_file_name="omit.mtz",
partial_occupancy=0.7)
xrs.shake_sites_in_place(0.1, selection=selection)
sites_new = building.run_real_space_annealing(xray_structure=xrs,
pdb_hierarchy=hierarchy,
selection=selection,
target_map=fofc_map,
d_min=f_obs.d_min(),
target_map_rsr=two_fofc_map,
debug=True)
hierarchy.atoms().set_xyz(sites_new)
hierarchy.write_pdb_file("anneal.pdb", crystal_symmetry=xrs)
print "wrote anneal.pdb and omit.mtz"
def exercise():
import mmtbx.utils
from iotbx.file_reader import any_file
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/CypA_refine_3.pdb", test=os.path.isfile
)
mtz_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/3k0n.mtz", test=os.path.isfile
)
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.construct_hierarchy()
xrs = pdb_in.file_object.xray_structure_simple()
mtz_in = any_file(mtz_file)
f_obs = mtz_in.file_server.miller_arrays[0].f_sq_as_f()
flags = mtz_in.file_server.miller_arrays[-1]
flags = flags.customized_copy(data=(flags.data() == 0))
assert (flags.data().count(True) / len(flags.data())) <= 0.1
f_obs, flags = f_obs.common_sets(other=flags)
fmodel = mmtbx.utils.fmodel_simple(
f_obs=f_obs, r_free_flags=flags, scattering_table="n_gaussian", xray_structures=[xrs]
)
fmodel.info().show_targets()
selection = hierarchy.atom_selection_cache().selection("chain A and resseq 111:115")
two_fofc_map, fofc_map, = disorder.get_partial_omit_map(
fmodel=fmodel, selection=selection, map_file_name="omit.mtz", partial_occupancy=0.7
)
xrs.shake_sites_in_place(0.1, selection=selection)
sites_new = building.run_real_space_annealing(
xray_structure=xrs,
pdb_hierarchy=hierarchy,
selection=selection,
target_map=fofc_map,
d_min=f_obs.d_min(),
target_map_rsr=two_fofc_map,
debug=True,
)
hierarchy.atoms().set_xyz(sites_new)
hierarchy.write_pdb_file("anneal.pdb", crystal_symmetry=xrs)
print "wrote anneal.pdb and omit.mtz"
def run(args, out=None):
if (out is None): out = sys.stdout
from mmtbx.building.alternate_conformations import resolve_build
from mmtbx.building import disorder
import mmtbx.maps.utils
import mmtbx.utils
cmdline = mmtbx.utils.cmdline_load_pdb_and_data(
args=args,
master_phil=master_phil,
process_pdb_file=True,
scattering_table="n_gaussian",
out=out)
params = cmdline.params
working_phil = master_phil.format(python_object=params)
master_phil.fetch_diff(source=working_phil).show(out=out)
fmodel = cmdline.fmodel
hierarchy = cmdline.pdb_hierarchy
sele_cache = hierarchy.atom_selection_cache()
if (params.selection is None):
raise Sorry("Please specify the selection parameter.")
selection = sele_cache.selection(params.selection)
assert (selection.count(True) > 0)
t1 = time.time()
two_fofc_map, fofc_map = disorder.get_partial_omit_map(
fmodel=fmodel,
selection=selection.iselection(),
selection_delete=None, #nearby_water_selection,
negate_surrounding=False,
partial_occupancy=params.partial_occupancy)
build = resolve_build.resolve_builder(
params=params.resolve_build,
pdb_hierarchy=hierarchy,
xray_structure=fmodel.xray_structure,
processed_pdb_file=cmdline.processed_pdb_file,
target_map=fofc_map,
selection=selection,
d_min=fmodel.f_obs().d_min(),
out=out)
def run (args, out=None) :
if (out is None) : out = sys.stdout
from mmtbx.building.alternate_conformations import resolve_build
from mmtbx.building import disorder
import mmtbx.maps.utils
import mmtbx.utils
cmdline = mmtbx.utils.cmdline_load_pdb_and_data(
args=args,
master_phil=master_phil,
process_pdb_file=True,
scattering_table="n_gaussian",
out=out)
params = cmdline.params
working_phil = master_phil.format(python_object=params)
master_phil.fetch_diff(source=working_phil).show(out=out)
fmodel = cmdline.fmodel
hierarchy = cmdline.pdb_hierarchy
sele_cache = hierarchy.atom_selection_cache()
if (params.selection is None) :
raise Sorry("Please specify the selection parameter.")
selection = sele_cache.selection(params.selection)
assert (selection.count(True) > 0)
t1 = time.time()
two_fofc_map, fofc_map = disorder.get_partial_omit_map(
fmodel=fmodel,
selection=selection.iselection(),
selection_delete=None,#nearby_water_selection,
negate_surrounding=False,
partial_occupancy=params.partial_occupancy)
build = resolve_build.resolve_builder(
params=params.resolve_build,
pdb_hierarchy=hierarchy,
xray_structure=fmodel.xray_structure,
processed_pdb_file=cmdline.processed_pdb_file,
target_map=fofc_map,
selection=selection,
d_min=fmodel.f_obs().d_min(),
out=out)