def run(args, external_params=None, out=sys.stdout):
from mmtbx.refinement import select_best_starting_model
import mmtbx.utils
from iotbx.file_reader import any_file
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_params(),
pdb_file_def="input.model",
reflection_file_def="input.xray_data.file_name",
usage_string="""\
mmtbx.select_best_starting_model data.mtz model1.pdb model2.pdb [...]
Given experimental data and a set of models, determines whether any of the
models can be refined directly (i.e. if isomorphous), and picks the one
with the best R-free below a specified cutoff. Will optionally perform
rigid-body refinement on suitable models if requested.""")
params = cmdline.work.extract()
validate_params(params)
hkl_in = any_file(params.input.xray_data.file_name)
data_and_flags = mmtbx.utils.determine_data_and_flags(
reflection_file_server=hkl_in.file_server,
parameters=params.input.xray_data,
data_parameter_scope="input.data",
flags_parameter_scope="input.data.r_free_flags",
log=out)
model_data = []
for file_name in params.input.model:
model_in = cmdline.get_file(file_name=file_name,
force_type="pdb").file_object
pdb_hierarchy = model_in.hierarchy
xray_structure = model_in.xray_structure_simple()
model_data.append((pdb_hierarchy, xray_structure))
# we can optionally pass a parameter block from elsewhere (e.g. phenix ligand
# pipeline) and just use this run() method to load files
params_ = external_params
if (params_ is None):
params_ = params
result = select_best_starting_model.select_model(
model_names=params.input.model,
model_data=model_data,
f_obs=data_and_flags.f_obs,
r_free_flags=data_and_flags.r_free_flags,
params=params_,
nproc=params.nproc,
skip_twin_detection=params.input.skip_twin_detection,
log=out)
if result.success() and params.output.write_files:
result.save_best_model(file_name=params.output.model_file_name)
print("", file=out)
print("Wrote best model to %s" % params.output.model_file_name,
file=out)
result.save_updated_data(file_name=params.output.data_file_name)
print("Wrote updated data to %s" % params.output.data_file_name,
file=out)
return result
def run (args, external_params=None, out=sys.stdout) :
from mmtbx.refinement import select_best_starting_model
import mmtbx.utils
from iotbx.file_reader import any_file
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_params(),
pdb_file_def="input.model",
reflection_file_def="input.xray_data.file_name",
usage_string="""\
mmtbx.select_best_starting_model data.mtz model1.pdb model2.pdb [...]
Given experimental data and a set of models, determines whether any of the
models can be refined directly (i.e. if isomorphous), and picks the one
with the best R-free below a specified cutoff. Will optionally perform
rigid-body refinement on suitable models if requested.""")
params = cmdline.work.extract()
validate_params(params)
hkl_in = any_file(params.input.xray_data.file_name)
data_and_flags = mmtbx.utils.determine_data_and_flags(
reflection_file_server=hkl_in.file_server,
parameters=params.input.xray_data,
data_parameter_scope="input.data",
flags_parameter_scope="input.data.r_free_flags",
log=out)
model_data = []
for file_name in params.input.model :
model_in = cmdline.get_file(
file_name=file_name,
force_type="pdb").file_object
pdb_hierarchy = model_in.hierarchy
xray_structure = model_in.xray_structure_simple()
model_data.append((pdb_hierarchy, xray_structure))
# we can optionally pass a parameter block from elsewhere (e.g. phenix ligand
# pipeline) and just use this run() method to load files
params_ = external_params
if (params_ is None) :
params_ = params
result = select_best_starting_model.select_model(
model_names=params.input.model,
model_data=model_data,
f_obs=data_and_flags.f_obs,
r_free_flags=data_and_flags.r_free_flags,
params=params_,
nproc=params.nproc,
skip_twin_detection=params.input.skip_twin_detection,
log=out)
if result.success() and params.output.write_files :
result.save_best_model(file_name=params.output.model_file_name)
print >> out, ""
print >> out, "Wrote best model to %s" % params.output.model_file_name
result.save_updated_data(file_name=params.output.data_file_name)
print >> out, "Wrote updated data to %s" % params.output.data_file_name
return result
def exercise_main():
from mmtbx.refinement import select_best_starting_model
from iotbx import file_reader
from cctbx import uctbx
from cctbx import sgtbx
from scitbx.array_family import flex
import random
unit_cell = (24.937, 8.866, 25.477, 90.00, 107.08, 90.00)
space_group = "P21"
pdb_base = """\
CRYST1 24.937 8.866 25.477 90.00 107.08 90.00 P 1 21 1
SCALE1 0.040101 0.000000 0.012321 0.00000
SCALE2 0.000000 0.112790 0.000000 0.00000
SCALE3 0.000000 0.000000 0.041062 0.00000
ATOM 1 N GLY A 1 8.992 0.474 -6.096 1.00 16.23 N
ATOM 2 CA GLY A 1 9.033 0.047 -4.707 1.00 16.20 C
ATOM 3 C GLY A 1 7.998 -1.029 -4.448 1.00 15.91 C
ATOM 4 O GLY A 1 7.548 -1.689 -5.385 1.00 16.11 O
ATOM 5 N ASN A 2 7.625 -1.218 -3.185 1.00 15.02 N
ATOM 6 CA ASN A 2 6.523 -2.113 -2.848 1.00 13.92 C
ATOM 7 C ASN A 2 5.220 -1.618 -3.428 1.00 12.24 C
ATOM 8 O ASN A 2 4.955 -0.418 -3.432 1.00 11.42 O
ATOM 9 CB ASN A 2 6.376 -2.261 -1.340 1.00 14.42 C
ATOM 10 CG ASN A 2 7.620 -2.786 -0.697 1.00 13.92 C
ATOM 11 OD1 ASN A 2 8.042 -3.915 -0.978 1.00 14.39 O
ATOM 12 ND2 ASN A 2 8.232 -1.975 0.168 1.00 12.78 N
ATOM 13 N ASN A 3 4.406 -2.553 -3.904 1.00 12.20 N
ATOM 14 CA ASN A 3 3.164 -2.226 -4.594 1.00 11.81 C
ATOM 15 C ASN A 3 1.925 -2.790 -3.910 1.00 10.59 C
ATOM 16 O ASN A 3 1.838 -3.991 -3.653 1.00 10.32 O
ATOM 17 CB ASN A 3 3.231 -2.727 -6.046 1.00 12.51 C
ATOM 18 CG ASN A 3 1.973 -2.405 -6.848 1.00 12.59 C
ATOM 19 OD1 ASN A 3 1.662 -1.239 -7.106 1.00 13.64 O
ATOM 20 ND2 ASN A 3 1.260 -3.443 -7.268 1.00 12.39 N
ATOM 21 N GLN A 4 0.973 -1.913 -3.608 1.00 10.34 N
ATOM 22 CA GLN A 4 -0.366 -2.335 -3.208 1.00 10.00 C
ATOM 23 C GLN A 4 -1.402 -1.637 -4.085 1.00 10.21 C
ATOM 24 O GLN A 4 -1.514 -0.414 -4.070 1.00 8.99 O
ATOM 25 CB GLN A 4 -0.656 -2.027 -1.736 1.00 10.00 C
ATOM 26 CG GLN A 4 -1.927 -2.705 -1.229 1.00 10.50 C
ATOM 27 CD GLN A 4 -2.482 -2.102 0.060 1.00 11.36 C
ATOM 28 OE1 GLN A 4 -2.744 -0.900 0.151 1.00 12.29 O
ATOM 29 NE2 GLN A 4 -2.684 -2.951 1.055 1.00 10.43 N
ATOM 30 N GLN A 5 -2.154 -2.406 -4.857 1.00 10.48 N
ATOM 31 CA GLN A 5 -3.247 -1.829 -5.630 1.00 11.24 C
ATOM 32 C GLN A 5 -4.591 -2.382 -5.178 1.00 11.40 C
ATOM 33 O GLN A 5 -4.789 -3.599 -5.092 1.00 11.94 O
ATOM 34 CB GLN A 5 -3.024 -2.023 -7.129 1.00 11.14 C
ATOM 35 CG GLN A 5 -1.852 -1.222 -7.653 1.00 10.65 C
ATOM 36 CD GLN A 5 -1.338 -1.748 -8.965 1.00 10.73 C
ATOM 37 OE1 GLN A 5 -0.794 -2.845 -9.028 1.00 10.14 O
ATOM 38 NE2 GLN A 5 -1.511 -0.968 -10.027 1.00 11.31 N
ATOM 39 N ASN A 6 -5.504 -1.471 -4.872 1.00 11.56 N
ATOM 40 CA ASN A 6 -6.809 -1.838 -4.359 1.00 12.07 C
ATOM 41 C ASN A 6 -7.856 -1.407 -5.353 1.00 13.18 C
ATOM 42 O ASN A 6 -8.257 -0.251 -5.362 1.00 13.64 O
ATOM 43 CB ASN A 6 -7.053 -1.149 -3.017 1.00 12.12 C
ATOM 44 CG ASN A 6 -5.966 -1.446 -1.998 1.00 12.31 C
ATOM 45 OD1 ASN A 6 -5.833 -2.579 -1.517 1.00 13.43 O
ATOM 46 ND2 ASN A 6 -5.198 -0.423 -1.645 1.00 11.88 N
ATOM 47 N TYR A 7 -8.298 -2.332 -6.193 1.00 14.34 N
ATOM 48 CA TYR A 7 -9.162 -1.980 -7.317 1.00 15.00 C
ATOM 49 C TYR A 7 -10.603 -1.792 -6.893 1.00 15.64 C
ATOM 50 O TYR A 7 -11.013 -2.278 -5.838 1.00 15.68 O
ATOM 51 CB TYR A 7 -9.064 -3.041 -8.412 1.00 15.31 C
ATOM 52 CG TYR A 7 -7.657 -3.197 -8.931 1.00 15.06 C
ATOM 53 CD1 TYR A 7 -6.785 -4.118 -8.368 1.00 15.24 C
ATOM 54 CD2 TYR A 7 -7.193 -2.400 -9.960 1.00 14.96 C
ATOM 55 CE1 TYR A 7 -5.489 -4.253 -8.830 1.00 14.94 C
ATOM 56 CE2 TYR A 7 -5.905 -2.526 -10.429 1.00 15.13 C
ATOM 57 CZ TYR A 7 -5.055 -3.451 -9.861 1.00 14.97 C
ATOM 58 OH TYR A 7 -3.768 -3.572 -10.335 1.00 14.93 O
ATOM 59 OXT TYR A 7 -11.378 -1.149 -7.601 1.00 15.89 O
TER
"""
pdb_base_water = """\
HETATM 64 O HOH S 1 -10.466 -2.347 -3.168 1.00 17.57 O
HETATM 65 O HOH S 2 6.469 1.081 -7.070 1.00 21.27 O
HETATM 66 O HOH S 3 -11.809 0.108 -9.956 1.00 27.52 O
HETATM 67 O HOH S 4 1.580 -3.455 -11.035 1.00 44.76 O
END
"""
with open("tst_start_model_base.pdb", "w") as f:
f.write(pdb_base + pdb_base_water)
params = """
high_resolution = 1.75
add_sigmas = True
pdb_file = tst_start_model_base.pdb
output {
label = F
type = *real complex
file_name = tst_start_model_base.mtz
}
"""
with open("tst_start_model_fmodel.eff", "w") as f:
f.write(params)
assert (easy_run.fully_buffered("phenix.fmodel tst_start_model_fmodel.eff"
).raise_if_errors().return_code == 0)
mtz_in = file_reader.any_file("tst_start_model_base.mtz")
f_obs = mtz_in.file_server.miller_arrays[0]
symm = f_obs.crystal_symmetry().customized_copy(
space_group_info=sgtbx.space_group_info("P2"))
f_obs = f_obs.customized_copy(crystal_symmetry=symm)
random.seed(12345) # XXX makes results more predictable
flags = f_obs.generate_r_free_flags(fraction=0.1)
mtz_data = f_obs.as_mtz_dataset(column_root_label="F")
mtz_data.add_miller_array(flags, column_root_label="FreeR_flag")
mtz_data.mtz_object().write("tst_start_model.mtz")
pdb_in = file_reader.any_file("tst_start_model_base.pdb")
hierarchy_in = pdb_in.file_object.hierarchy
xrs_in = pdb_in.file_object.xray_structure_simple()
selection = hierarchy_in.atom_selection_cache().selection
# Model 1: very few changes, but shifted by (1,0,0.5)
symm2 = xrs_in.crystal_symmetry().customized_copy(
unit_cell=uctbx.unit_cell((24.932, 8.841, 25.501, 90.00, 107.5,
90.00)))
#u_iso = xrs_in.extract_u_iso_or_u_equiv()
#xrs_out = xrs_in.deep_copy_scatterers().set_u_iso(
# selection=flex.bool(u_iso.size(), True), values=u_iso*1.1)
xrs_out = xrs_in.deep_copy_scatterers()
sites_cart = xrs_out.sites_cart()
sites_cart += flex.vec3_double(sites_cart.size(), (1.0, 0.0, 0.5))
xrs_out.set_sites_cart(sites_cart)
hierarchy_out = hierarchy_in.deep_copy()
hierarchy_out.adopt_xray_structure(xrs_out)
with open("tst_start_model_1.pdb", "w") as f:
f.write(hierarchy_out.as_pdb_string(crystal_symmetry=symm2))
# Model 2: no sidechains
mc_sele = selection("(name N or name C or name O or name CA or name CB)")
hierarchy_out = hierarchy_in.select(mc_sele)
xrs_out = xrs_in.select(mc_sele)
with open("tst_start_model_2.pdb", "w") as f:
f.write(hierarchy_out.as_pdb_string(crystal_symmetry=xrs_out))
# Model 3: P1 symmetry
symm3 = xrs_in.crystal_symmetry().customized_copy(
space_group_info=sgtbx.space_group_info("P1"))
with open("tst_start_model_3.pdb", "w") as f:
f.write(hierarchy_out.as_pdb_string(crystal_symmetry=symm3))
# Model 4: shaken coordinates and ADPs
def random_double(size, factor=1):
d = flex.double()
for x in range(size):
d.append(random.random() * factor)
return d
xrs_out = xrs_in.customized_copy()
xrs_out.shake_sites_in_place(0.3, random_double=random_double)
xrs_out.shake_adp()
hierarchy_out = hierarchy_in.deep_copy()
hierarchy_out.adopt_xray_structure(xrs_out)
with open("tst_start_model_4.pdb", "w") as f:
f.write(hierarchy_out.as_pdb_string(crystal_symmetry=xrs_out))
# Model 5: perfect, but missing CRYST1
with open("tst_start_model_5.pdb", "w") as f:
f.write(hierarchy_in.as_pdb_string())
# run method
params = select_best_starting_model.master_phil.extract()
params.rigid_body_refine = False
model_names = [
"tst_start_model_1.pdb",
"tst_start_model_2.pdb",
"tst_start_model_3.pdb",
"tst_start_model_4.pdb",
"tst_start_model_5.pdb",
]
result = select_best_starting_model.select_model(model_names=model_names,
model_data=None,
f_obs=f_obs,
r_free_flags=flags,
params=params,
skip_twin_detection=True,
log=null_out())
# result.show(verbose=True)
assert (result.best_model_name == "tst_start_model_4.pdb"
), result.best_model_name
params.rigid_body_refine = True
result = select_best_starting_model.select_model(model_names=model_names,
model_data=None,
f_obs=f_obs,
r_free_flags=flags,
params=params,
skip_twin_detection=True,
log=null_out())
# result.show(verbose=True)
assert (result.best_model_name == "tst_start_model_1.pdb"
), result.best_model_name
def exercise_main():
from mmtbx.refinement import select_best_starting_model
from iotbx import file_reader
from cctbx import uctbx
from cctbx import sgtbx
from scitbx.array_family import flex
import random
unit_cell = (24.937, 8.866, 25.477, 90.00, 107.08, 90.00)
space_group = "P21"
pdb_base = """\
CRYST1 24.937 8.866 25.477 90.00 107.08 90.00 P 1 21 1
SCALE1 0.040101 0.000000 0.012321 0.00000
SCALE2 0.000000 0.112790 0.000000 0.00000
SCALE3 0.000000 0.000000 0.041062 0.00000
ATOM 1 N GLY A 1 8.992 0.474 -6.096 1.00 16.23 N
ATOM 2 CA GLY A 1 9.033 0.047 -4.707 1.00 16.20 C
ATOM 3 C GLY A 1 7.998 -1.029 -4.448 1.00 15.91 C
ATOM 4 O GLY A 1 7.548 -1.689 -5.385 1.00 16.11 O
ATOM 5 N ASN A 2 7.625 -1.218 -3.185 1.00 15.02 N
ATOM 6 CA ASN A 2 6.523 -2.113 -2.848 1.00 13.92 C
ATOM 7 C ASN A 2 5.220 -1.618 -3.428 1.00 12.24 C
ATOM 8 O ASN A 2 4.955 -0.418 -3.432 1.00 11.42 O
ATOM 9 CB ASN A 2 6.376 -2.261 -1.340 1.00 14.42 C
ATOM 10 CG ASN A 2 7.620 -2.786 -0.697 1.00 13.92 C
ATOM 11 OD1 ASN A 2 8.042 -3.915 -0.978 1.00 14.39 O
ATOM 12 ND2 ASN A 2 8.232 -1.975 0.168 1.00 12.78 N
ATOM 13 N ASN A 3 4.406 -2.553 -3.904 1.00 12.20 N
ATOM 14 CA ASN A 3 3.164 -2.226 -4.594 1.00 11.81 C
ATOM 15 C ASN A 3 1.925 -2.790 -3.910 1.00 10.59 C
ATOM 16 O ASN A 3 1.838 -3.991 -3.653 1.00 10.32 O
ATOM 17 CB ASN A 3 3.231 -2.727 -6.046 1.00 12.51 C
ATOM 18 CG ASN A 3 1.973 -2.405 -6.848 1.00 12.59 C
ATOM 19 OD1 ASN A 3 1.662 -1.239 -7.106 1.00 13.64 O
ATOM 20 ND2 ASN A 3 1.260 -3.443 -7.268 1.00 12.39 N
ATOM 21 N GLN A 4 0.973 -1.913 -3.608 1.00 10.34 N
ATOM 22 CA GLN A 4 -0.366 -2.335 -3.208 1.00 10.00 C
ATOM 23 C GLN A 4 -1.402 -1.637 -4.085 1.00 10.21 C
ATOM 24 O GLN A 4 -1.514 -0.414 -4.070 1.00 8.99 O
ATOM 25 CB GLN A 4 -0.656 -2.027 -1.736 1.00 10.00 C
ATOM 26 CG GLN A 4 -1.927 -2.705 -1.229 1.00 10.50 C
ATOM 27 CD GLN A 4 -2.482 -2.102 0.060 1.00 11.36 C
ATOM 28 OE1 GLN A 4 -2.744 -0.900 0.151 1.00 12.29 O
ATOM 29 NE2 GLN A 4 -2.684 -2.951 1.055 1.00 10.43 N
ATOM 30 N GLN A 5 -2.154 -2.406 -4.857 1.00 10.48 N
ATOM 31 CA GLN A 5 -3.247 -1.829 -5.630 1.00 11.24 C
ATOM 32 C GLN A 5 -4.591 -2.382 -5.178 1.00 11.40 C
ATOM 33 O GLN A 5 -4.789 -3.599 -5.092 1.00 11.94 O
ATOM 34 CB GLN A 5 -3.024 -2.023 -7.129 1.00 11.14 C
ATOM 35 CG GLN A 5 -1.852 -1.222 -7.653 1.00 10.65 C
ATOM 36 CD GLN A 5 -1.338 -1.748 -8.965 1.00 10.73 C
ATOM 37 OE1 GLN A 5 -0.794 -2.845 -9.028 1.00 10.14 O
ATOM 38 NE2 GLN A 5 -1.511 -0.968 -10.027 1.00 11.31 N
ATOM 39 N ASN A 6 -5.504 -1.471 -4.872 1.00 11.56 N
ATOM 40 CA ASN A 6 -6.809 -1.838 -4.359 1.00 12.07 C
ATOM 41 C ASN A 6 -7.856 -1.407 -5.353 1.00 13.18 C
ATOM 42 O ASN A 6 -8.257 -0.251 -5.362 1.00 13.64 O
ATOM 43 CB ASN A 6 -7.053 -1.149 -3.017 1.00 12.12 C
ATOM 44 CG ASN A 6 -5.966 -1.446 -1.998 1.00 12.31 C
ATOM 45 OD1 ASN A 6 -5.833 -2.579 -1.517 1.00 13.43 O
ATOM 46 ND2 ASN A 6 -5.198 -0.423 -1.645 1.00 11.88 N
ATOM 47 N TYR A 7 -8.298 -2.332 -6.193 1.00 14.34 N
ATOM 48 CA TYR A 7 -9.162 -1.980 -7.317 1.00 15.00 C
ATOM 49 C TYR A 7 -10.603 -1.792 -6.893 1.00 15.64 C
ATOM 50 O TYR A 7 -11.013 -2.278 -5.838 1.00 15.68 O
ATOM 51 CB TYR A 7 -9.064 -3.041 -8.412 1.00 15.31 C
ATOM 52 CG TYR A 7 -7.657 -3.197 -8.931 1.00 15.06 C
ATOM 53 CD1 TYR A 7 -6.785 -4.118 -8.368 1.00 15.24 C
ATOM 54 CD2 TYR A 7 -7.193 -2.400 -9.960 1.00 14.96 C
ATOM 55 CE1 TYR A 7 -5.489 -4.253 -8.830 1.00 14.94 C
ATOM 56 CE2 TYR A 7 -5.905 -2.526 -10.429 1.00 15.13 C
ATOM 57 CZ TYR A 7 -5.055 -3.451 -9.861 1.00 14.97 C
ATOM 58 OH TYR A 7 -3.768 -3.572 -10.335 1.00 14.93 O
ATOM 59 OXT TYR A 7 -11.378 -1.149 -7.601 1.00 15.89 O
TER
"""
pdb_base_water = """\
HETATM 64 O HOH S 1 -10.466 -2.347 -3.168 1.00 17.57 O
HETATM 65 O HOH S 2 6.469 1.081 -7.070 1.00 21.27 O
HETATM 66 O HOH S 3 -11.809 0.108 -9.956 1.00 27.52 O
HETATM 67 O HOH S 4 1.580 -3.455 -11.035 1.00 44.76 O
END
"""
open("tst_start_model_base.pdb", "w").write(pdb_base + pdb_base_water)
params = """
high_resolution = 1.75
add_sigmas = True
pdb_file = tst_start_model_base.pdb
output {
label = F
type = *real complex
file_name = tst_start_model_base.mtz
}
"""
open("tst_start_model_fmodel.eff", "w").write(params)
assert easy_run.fully_buffered("phenix.fmodel tst_start_model_fmodel.eff").raise_if_errors().return_code == 0
mtz_in = file_reader.any_file("tst_start_model_base.mtz")
f_obs = mtz_in.file_server.miller_arrays[0]
symm = f_obs.crystal_symmetry().customized_copy(space_group_info=sgtbx.space_group_info("P2"))
f_obs = f_obs.customized_copy(crystal_symmetry=symm)
random.seed(12345) # XXX makes results more predictable
flags = f_obs.generate_r_free_flags(fraction=0.1)
mtz_data = f_obs.as_mtz_dataset(column_root_label="F")
mtz_data.add_miller_array(flags, column_root_label="FreeR_flag")
mtz_data.mtz_object().write("tst_start_model.mtz")
pdb_in = file_reader.any_file("tst_start_model_base.pdb")
hierarchy_in = pdb_in.file_object.hierarchy
xrs_in = pdb_in.file_object.xray_structure_simple()
selection = hierarchy_in.atom_selection_cache().selection
# Model 1: very few changes, but shifted by (1,0,0.5)
symm2 = xrs_in.crystal_symmetry().customized_copy(
unit_cell=uctbx.unit_cell((24.932, 8.841, 25.501, 90.00, 107.5, 90.00))
)
# u_iso = xrs_in.extract_u_iso_or_u_equiv()
# xrs_out = xrs_in.deep_copy_scatterers().set_u_iso(
# selection=flex.bool(u_iso.size(), True), values=u_iso*1.1)
xrs_out = xrs_in.deep_copy_scatterers()
sites_cart = xrs_out.sites_cart()
sites_cart += flex.vec3_double(sites_cart.size(), (1.0, 0.0, 0.5))
xrs_out.set_sites_cart(sites_cart)
hierarchy_out = hierarchy_in.deep_copy()
hierarchy_out.adopt_xray_structure(xrs_out)
open("tst_start_model_1.pdb", "w").write(hierarchy_out.as_pdb_string(crystal_symmetry=symm2))
# Model 2: no sidechains
mc_sele = selection("(name N or name C or name O or name CA or name CB)")
hierarchy_out = hierarchy_in.select(mc_sele)
xrs_out = xrs_in.select(mc_sele)
open("tst_start_model_2.pdb", "w").write(hierarchy_out.as_pdb_string(crystal_symmetry=xrs_out))
# Model 3: P1 symmetry
symm3 = xrs_in.crystal_symmetry().customized_copy(space_group_info=sgtbx.space_group_info("P1"))
open("tst_start_model_3.pdb", "w").write(hierarchy_out.as_pdb_string(crystal_symmetry=symm3))
# Model 4: shaken coordinates and ADPs
def random_double(size, factor=1):
d = flex.double()
for x in range(size):
d.append(random.random() * factor)
return d
xrs_out = xrs_in.customized_copy()
xrs_out.shake_sites_in_place(0.3, random_double=random_double)
xrs_out.shake_adp()
hierarchy_out = hierarchy_in.deep_copy()
hierarchy_out.adopt_xray_structure(xrs_out)
open("tst_start_model_4.pdb", "w").write(hierarchy_out.as_pdb_string(crystal_symmetry=xrs_out))
# Model 5: perfect, but missing CRYST1
open("tst_start_model_5.pdb", "w").write(hierarchy_in.as_pdb_string())
# run method
params = select_best_starting_model.master_phil.extract()
params.rigid_body_refine = False
model_names = [
"tst_start_model_1.pdb",
"tst_start_model_2.pdb",
"tst_start_model_3.pdb",
"tst_start_model_4.pdb",
"tst_start_model_5.pdb",
]
result = select_best_starting_model.select_model(
model_names=model_names,
model_data=None,
f_obs=f_obs,
r_free_flags=flags,
params=params,
skip_twin_detection=True,
log=null_out(),
)
# result.show(verbose=True)
assert result.best_model_name == "tst_start_model_4.pdb", result.best_model_name
params.rigid_body_refine = True
result = select_best_starting_model.select_model(
model_names=model_names,
model_data=None,
f_obs=f_obs,
r_free_flags=flags,
params=params,
skip_twin_detection=True,
log=null_out(),
)
# result.show(verbose=True)
assert result.best_model_name == "tst_start_model_1.pdb", result.best_model_name