def exercise_space_group_handling():
flex.set_random_seed(123456)
random.seed(123456)
base = "tst_cc_star_space_group"
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=model_1yjp)
xrs = pdb_in.xray_structure_simple()
xrs.set_inelastic_form_factors(photon=1.54, table="sasaki")
fc = abs(xrs.structure_factors(d_min=1.5).f_calc()).average_bijvoet_mates()
fc.set_observation_type_xray_amplitude()
flags = fc.generate_r_free_flags()
mtz = fc.as_mtz_dataset(column_root_label="F")
mtz.add_miller_array(flags, column_root_label="FreeR_flag")
mtz.mtz_object().write(base + ".mtz")
xrs_p1 = xrs.expand_to_p1()
xrs_p1.shake_sites_in_place(rms_difference=0.1)
fc_p1 = xrs_p1.structure_factors(d_min=1.4).f_calc()
fc_p1_extra = fc_p1.randomize_amplitude_and_phase(amplitude_error=1.0,
phase_error_deg=0,
random_seed=123456)
fc_p1 = abs(
fc_p1.concatenate(other=fc_p1_extra)).sort(by_value="packed_indices")
fc_p1.set_observation_type_xray_amplitude()
sg_p2 = sgtbx.space_group_info("P2")
ic = fc_p1.f_as_f_sq().customized_copy(space_group_info=sg_p2,
sigmas=flex.double(
fc_p1.size(), 10.0))
ic.export_as_scalepack_unmerged(file_name=base + ".sca")
open(base + ".pdb", "w").write(model_1yjp)
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s.sca" % base,
]
cc_star.run(args=args, out=null_out())
# now with .sca in P1 (raises Sorry)
ic2 = fc_p1.f_as_f_sq().customized_copy(
sigmas=flex.double(fc_p1.size(), 10.0))
ic2.export_as_scalepack_unmerged(file_name=base + "_p1.sca")
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s_p1.sca" % base,
]
try:
cc_star.run(args=args, out=null_out())
except Sorry, s:
assert (
str(s) ==
"Incompatible space groups in merged and unmerged data:P 1 21 1 versus P 1"
), s
def exercise_space_group_handling () :
flex.set_random_seed(123456)
random.seed(123456)
base = "tst_cc_star_space_group"
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=model_1yjp)
xrs = pdb_in.xray_structure_simple()
xrs.set_inelastic_form_factors(
photon=1.54,
table="sasaki")
fc = abs(xrs.structure_factors(d_min=1.5).f_calc()).average_bijvoet_mates()
fc.set_observation_type_xray_amplitude()
flags = fc.generate_r_free_flags()
mtz = fc.as_mtz_dataset(column_root_label="F")
mtz.add_miller_array(flags, column_root_label="FreeR_flag")
mtz.mtz_object().write(base + ".mtz")
xrs_p1 = xrs.expand_to_p1()
xrs_p1.shake_sites_in_place(rms_difference=0.1)
fc_p1 = xrs_p1.structure_factors(d_min=1.4).f_calc()
fc_p1_extra = fc_p1.randomize_amplitude_and_phase(amplitude_error=1.0,
phase_error_deg=0,
random_seed=123456)
fc_p1 = abs(fc_p1.concatenate(other=fc_p1_extra)).sort(
by_value="packed_indices")
fc_p1.set_observation_type_xray_amplitude()
sg_p2 = sgtbx.space_group_info("P2")
ic = fc_p1.f_as_f_sq().customized_copy(
space_group_info=sg_p2,
sigmas=flex.double(fc_p1.size(), 10.0))
ic.export_as_scalepack_unmerged(file_name=base + ".sca")
open(base + ".pdb", "w").write(model_1yjp)
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s.sca" % base,
]
cc_star.run(args=args, out=null_out())
# now with .sca in P1 (raises Sorry)
ic2 = fc_p1.f_as_f_sq().customized_copy(
sigmas=flex.double(fc_p1.size(), 10.0))
ic2.export_as_scalepack_unmerged(file_name=base + "_p1.sca")
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s_p1.sca" % base,
]
try :
cc_star.run(args=args, out=null_out())
except Sorry, s :
assert (str(s) == "Incompatible space groups in merged and unmerged data:P 1 21 1 versus P 1"), s
def old_run(args, out=None):
import iotbx.phil
if (out is None):
out = sys.stdout
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
pdb_file_def="input.pdb_file",
seq_file_def="input.seq_file")
params = cmdline.work.extract()
cmdline.work.show()
if params.output.cif_file is None:
params.output.cif_file = os.path.splitext(
params.input.pdb_file)[0] + ".deposit.cif"
model_vs_sequence.validate_params(params)
pdb_input = mmcif.cif_input(file_name=params.input.pdb_file)
pdb_hierarchy = pdb_input.construct_hierarchy()
cif_model = pdb_input.cif_model
cif_block = pdb_input.cif_block
seq_in = any_file(params.input.seq_file, force_type="seq")
seq_in.check_file_type("seq")
sequences = seq_in.file_object
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences,
crystal_symmetry=pdb_input.crystal_symmetry(),
alignment_params=params)
block_name = cif_model.keys()[0]
def float_or_none(string):
try:
return float(string)
except TypeError:
return None
d_min_from_cif = float_or_none(cif_block.get('_refine.ls_d_res_high'))
d_max_from_cif = float_or_none(cif_block.get('_refine.ls_d_res_low'))
# XXX maybe the values from the CIF (i.e. those actually used in the refinement)
# should override the input params?
if params.high_resolution is not None:
params.high_resolution = d_min_from_cif
if params.low_resolution is not None:
params.low_resolution = d_max_from_cif
if params.input.unmerged_data is not None:
from mmtbx.command_line import cc_star
result = cc_star.run(params=params.input, out=out)
cif_block.update(result.as_cif_block())
cif_model[block_name].update(cif_block)
cif_model[block_name].sort(key=category_sort_function)
print >> out, "Writing updated CIF file:"
print >> out, " " + params.output.cif_file
with open(params.output.cif_file, "wb") as f:
print >> f, cif_model
return
def run(args, out=None):
import iotbx.phil
if (out is None) :
out = sys.stdout
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
pdb_file_def="input.pdb_file",
seq_file_def="input.seq_file"
)
params = cmdline.work.extract()
cmdline.work.show()
if params.output.cif_file is None:
params.output.cif_file = os.path.splitext(params.input.pdb_file)[0] + ".deposit.cif"
model_vs_sequence.validate_params(params)
pdb_input = mmcif.cif_input(file_name=params.input.pdb_file)
pdb_hierarchy = pdb_input.construct_hierarchy()
cif_model = pdb_input.cif_model
cif_block = pdb_input.cif_block
seq_in = any_file(params.input.seq_file, force_type="seq")
seq_in.check_file_type("seq")
sequences = seq_in.file_object
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences, crystal_symmetry=pdb_input.crystal_symmetry(),
alignment_params=params)
block_name = cif_model.keys()[0]
def float_or_none(string):
try: return float(string)
except TypeError: return None
d_min_from_cif = float_or_none(cif_block.get('_refine.ls_d_res_high'))
d_max_from_cif = float_or_none(cif_block.get('_refine.ls_d_res_low'))
# XXX maybe the values from the CIF (i.e. those actually used in the refinement)
# should override the input params?
if params.high_resolution is not None:
params.high_resolution = d_min_from_cif
if params.low_resolution is not None:
params.low_resolution = d_max_from_cif
if params.input.unmerged_data is not None:
from mmtbx.command_line import cc_star
result = cc_star.run(params=params.input, out=out)
cif_block.update(result.as_cif_block())
cif_model[block_name].update(cif_block)
cif_model[block_name].sort(key=category_sort_function)
print >> out, "Writing updated CIF file:"
print >> out, " " + params.output.cif_file
with open(params.output.cif_file, "wb") as f:
print >> f, cif_model
return
assert (
str(s) ==
"Incompatible space groups in merged and unmerged data:P 1 21 1 versus P 1"
), s
else:
raise Exception_expected
# now with CIF (complete symmetry)
f = open(base + ".cif", "w")
ic.as_cif_simple(array_type="meas", out=f)
f.close()
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s.cif" % base,
]
cc_star.run(args=args, out=null_out())
# bad unit cell
uc2 = uctbx.unit_cell((23, 6.5, 23.5, 90, 108, 90))
ic3 = ic.customized_copy(unit_cell=uc2)
f = open(base + "_new_uc.cif", "w")
ic3.as_cif_simple(array_type="meas", out=f)
f.close()
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s_new_uc.cif" % base,
]
try:
cc_star.run(args=args, out=null_out())
except Sorry, s:
assert ("Incompatible symmetry definitions:" in str(s)), s
cc_star.run(args=args, out=null_out()) except Sorry, s : assert (str(s) == "Incompatible space groups in merged and unmerged data:P 1 21 1 versus P 1"), s else : raise Exception_expected # now with CIF (complete symmetry) f = open(base + ".cif", "w") ic.as_cif_simple(array_type="meas", out=f) f.close() args = [ base + ".mtz", base + ".pdb", "unmerged_data=%s.cif" % base, ] cc_star.run(args=args, out=null_out()) # bad unit cell uc2 = uctbx.unit_cell((23,6.5,23.5,90,108,90)) ic3 = ic.customized_copy(unit_cell=uc2) f = open(base + "_new_uc.cif", "w") ic3.as_cif_simple(array_type="meas", out=f) f.close() args = [ base + ".mtz", base + ".pdb", "unmerged_data=%s_new_uc.cif" % base, ] try : cc_star.run(args=args, out=null_out()) except Sorry, s :
