def run(args, log=sys.stdout):
if (len(args) == 0):
print >> log, legend
defaults(log=log)
return
#
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(
args=args, log=sys.stdout, master_params=parsed)
params = processed_args.params.extract()
reflection_files = processed_args.reflection_files
if (len(reflection_files) == 0):
if (params.hkl_file is None):
raise Sorry("No reflection file found.")
else:
hkl_in = file_reader.any_file(params.hkl_file, force_type="hkl")
hkl_in.assert_file_type("hkl")
reflection_files = [hkl_in.file_object]
crystal_symmetry = processed_args.crystal_symmetry
if (crystal_symmetry is None):
if (params.space_group is not None) and (params.unit_cell is not None):
from cctbx import crystal
crystal_symmetry = crystal.symmetry(
space_group_info=params.space_group,
unit_cell=params.unit_cell)
else:
raise Sorry("No crystal symmetry found.")
if (len(processed_args.pdb_file_names) == 0):
if (params.pdb_file is None):
raise Sorry("No model file found.")
else:
pdb_file_names = [params.pdb_file]
else:
pdb_file_names = processed_args.pdb_file_names
#
rfs = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=StringIO())
parameters = mmtbx.utils.data_and_flags_master_params().extract()
parameters.labels = params.f_obs_label
parameters.r_free_flags.label = params.r_free_flags_label
determine_data_and_flags_result = mmtbx.utils.determine_data_and_flags(
reflection_file_server=rfs,
parameters=parameters,
keep_going=True,
log=StringIO())
f_obs = determine_data_and_flags_result.f_obs
print "Input data:"
print " Iobs or Fobs:", f_obs.info().labels
r_free_flags = determine_data_and_flags_result.r_free_flags
print " Free-R flags:", r_free_flags.info().labels
#
parameters = mmtbx.utils.experimental_phases_params.extract()
parameters.labels = params.hendrickson_lattman_coefficients_label
experimental_phases_result = mmtbx.utils.determine_experimental_phases(
reflection_file_server=rfs,
parameters=parameters,
log=StringIO(),
parameter_scope="",
working_point_group=None,
symmetry_safety_check=True,
ignore_all_zeros=True)
if (experimental_phases_result is not None):
print " HL coefficients:", experimental_phases_result.info().labels
experimental_phases = extract_experimental_phases(
experimental_phases=experimental_phases_result, f_obs=f_obs)
#
if (r_free_flags is None):
r_free_flags = f_obs.array(data=flex.bool(f_obs.data().size(), False))
#
pdb_inp = mmtbx.utils.pdb_inp_from_multiple_files(pdb_file_names,
log=sys.stdout)
model = mmtbx.model.manager(model_input=pdb_inp,
process_input=False,
crystal_symmetry=crystal_symmetry,
log=sys.stdout)
if (model.get_number_of_models() > 1): #XXX support multi-models
raise Sorry("Multiple model file not supported in this tool.")
# XXX Twining not supported
xray_structure = model.get_xray_structure()
if (not xray_structure.unit_cell().is_similar_to(f_obs.unit_cell())):
raise Sorry(
"The unit cells in the model and reflections files are not " +
"isomorphous.")
print "Input model:"
print " number of atoms:", xray_structure.scatterers().size()
fmodel = mmtbx.f_model.manager(xray_structure=xray_structure,
r_free_flags=r_free_flags,
f_obs=f_obs,
abcd=experimental_phases)
fmodel.update_all_scales(
update_f_part1=True,
remove_outliers=params.remove_f_obs_outliers,
bulk_solvent_and_scaling=params.bulk_solvent_and_scaling)
print "Overall statistics:"
fmodel.info().show_all()
#
print "Output data:"
if (params.output_file_name is not None):
output_file_name = params.output_file_name
else:
pdb_file_bn = os.path.basename(pdb_file_names[0])
hkl_file_bn = os.path.basename(reflection_files[0].file_name())
try:
pdb_file_prefix = pdb_file_bn[:pdb_file_bn.index(".")]
except ValueError:
pdb_file_prefix = pdb_file_bn
try:
hkl_file_prefix = hkl_file_bn[:hkl_file_bn.index(".")]
except ValueError:
hkl_file_prefix = hkl_file_bn
output_file_name = "%s_%s.mtz" % (pdb_file_prefix, hkl_file_prefix)
print " file name:", output_file_name
print " to see the contnt of %s:" % output_file_name
print " phenix.mtz.dump %s" % output_file_name
out = open(output_file_name, "w")
fmodel.export(out=out)
out.close()
print "All done."
return output_file_name
def run(args, log=sys.stdout):
print >> log, "-" * 79
print >> log, legend
print >> log, "-" * 79
inputs = mmtbx.utils.process_command_line_args(
args=args, master_params=master_params())
params = inputs.params.extract()
# estimate resolution
d_min = params.resolution
broadcast(m="Map resolution:", log=log)
if (d_min is None):
raise Sorry("Resolution is required.")
print >> log, " d_min: %6.4f" % d_min
# model
broadcast(m="Input PDB:", log=log)
file_names = inputs.pdb_file_names
if (len(file_names) != 1): raise Sorry("PDB file has to given.")
if (inputs.crystal_symmetry is None):
raise Sorry("No crystal symmetry defined.")
pdb_inp = iotbx.pdb.input(file_name=file_names[0])
model = mmtbx.model.manager(model_input=pdb_inp,
crystal_symmetry=inputs.crystal_symmetry,
build_grm=True)
if model.get_number_of_models() > 1:
raise Sorry("Only one model allowed.")
model.setup_scattering_dictionaries(
scattering_table=params.scattering_table)
model.get_xray_structure().show_summary(f=log, prefix=" ")
broadcast(m="Input map:", log=log)
if (inputs.ccp4_map is None): raise Sorry("Map file has to given.")
inputs.ccp4_map.show_summary(prefix=" ")
map_data = inputs.ccp4_map.map_data()
print >> log, " Actual map (min,max,mean):", \
map_data.as_1d().min_max_mean().as_tuple()
make_sub_header("Histogram of map values", out=log)
md = map_data.as_1d()
show_histogram(data=md,
n_slots=10,
data_min=flex.min(md),
data_max=flex.max(md),
log=log)
# shift origin if needed
soin = maptbx.shift_origin_if_needed(
map_data=map_data,
sites_cart=model.get_sites_cart(),
crystal_symmetry=model.crystal_symmetry())
map_data = soin.map_data
model.set_sites_cart(soin.sites_cart, update_grm=True)
####
# Compute and show all stats
####
broadcast(m="Model statistics:", log=log)
make_sub_header("Overall", out=log)
info = mmtbx.model.statistics.info(model=model)
info.geometry.show()
# XXX - these are not available anymore due to refactoring
# make_sub_header("Histogram of devations from ideal bonds", out=log)
# show_histogram(data=ms.bond_deltas, n_slots=10, data_min=0, data_max=0.2,
# log=log)
# #
# make_sub_header("Histogram of devations from ideal angles", out=log)
# show_histogram(data=ms.angle_deltas, n_slots=10, data_min=0, data_max=30.,
# log=log)
# #
# make_sub_header("Histogram of non-bonded distances", out=log)
# show_histogram(data=ms.nonbonded_distances, n_slots=10, data_min=0,
# data_max=5., log=log)
#
make_sub_header("Histogram of ADPs", out=log)
info.adp.show(log=log)
# bs = xrs.extract_u_iso_or_u_equiv()*adptbx.u_as_b(1.)
# show_histogram(data=bs, n_slots=10, data_min=flex.min(bs),
# data_max=flex.max(bs), log=log)
#
# Compute CC
broadcast(m="Map-model CC (overall):", log=log)
five_cc_result = mmtbx.maps.correlation.five_cc(
map=map_data, xray_structure=model.get_xray_structure(), d_min=d_min)
atom_radius = five_cc_result.atom_radius
if atom_radius is None:
atom_radius = five_cc_result._atom_radius()
print >> log, " CC_mask : %6.4f" % five_cc_result.result.cc_mask
print >> log, " CC_volume: %6.4f" % five_cc_result.result.cc_volume
print >> log, " CC_peaks : %6.4f" % five_cc_result.result.cc_peaks
# Compute FSC(map, model)
broadcast(m="Model-map FSC:", log=log)
fsc = mmtbx.maps.correlation.fsc_model_vs_map(
xray_structure=model.get_xray_structure(),
map=map_data,
atom_radius=atom_radius,
d_min=d_min)
fsc.show(prefix=" ")
# Local CC
cc_calculator = mmtbx.maps.correlation.from_map_and_xray_structure_or_fmodel(
xray_structure=model.get_xray_structure(),
map_data=map_data,
d_min=d_min)
broadcast(m="Map-model CC (local):", log=log)
# per residue
print >> log, "Per residue:"
residue_results = list()
ph = model.get_hierarchy()
xrs = model.get_xray_structure()
for rg in ph.residue_groups():
cc = cc_calculator.cc(selection=rg.atoms().extract_i_seq())
chain_id = rg.parent().id
print >> log, " chain id: %s resid %s: %6.4f" % (chain_id, rg.resid(),
cc)
# per chain
print >> log, "Per chain:"
for chain in ph.chains():
print >> log, " chain %s: %6.4f" % (
chain.id,
cc_calculator.cc(selection=chain.atoms().extract_i_seq()))
# per residue detailed counts
print >> log, "Per residue (histogram):"
crystal_gridding = maptbx.crystal_gridding(
unit_cell=xrs.unit_cell(),
space_group_info=xrs.space_group_info(),
pre_determined_n_real=map_data.accessor().all())
f_calc = xrs.structure_factors(d_min=d_min).f_calc()
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_calc)
fft_map.apply_sigma_scaling()
map_model = fft_map.real_map_unpadded()
sites_cart = xrs.sites_cart()
cc_per_residue = flex.double()
for rg in ph.residue_groups():
cc = mmtbx.maps.correlation.from_map_map_atoms(
map_1=map_data,
map_2=map_model,
sites_cart=sites_cart.select(rg.atoms().extract_i_seq()),
unit_cell=xrs.unit_cell(),
radius=2.)
cc_per_residue.append(cc)
show_histogram(data=cc_per_residue,
n_slots=10,
data_min=-1.,
data_max=1.0,
log=log)
