def __init__(self,pdb_file,hklmtz_file,
detail,high_resolution=None,mdb_document=None,pdb_code=None,
do_flips=False) :
assert detail in ['file','residue'],detail
assert type(do_flips) == bool
self.pdb_file = pdb_file
self.hklmtz_file = hklmtz_file
self.detail = detail
self.pdb_code = pdb_code
self.high_resolution = high_resolution
self.do_flips = do_flips
if not pdb_code : self.pdb_code = 'N/A'
pdb_in = file_reader.any_file(pdb_file)
self.hierarchy = pdb_in.file_object.hierarchy
args = [self.pdb_file]
if self.hklmtz_file : args.append(self.hklmtz_file)
self.cmdline = load_model_and_data(
args=args,
master_phil=generate_master_phil_with_inputs(""),
require_data=False,
create_fmodel=True,
process_pdb_file=True,
prefer_anomalous=True)
# keys are res ids and values are MDBResidue objects.
if self.detail == 'residue' :
self.initiate_residues()
self.set_mdb_document(mdb_document)
def _main(args, out=sys.stdout):
"""
Main entry point to this script.
Parameters
----------
args : list of str
List of arguments, should not include the first argument with the
executable name.
out : file, optional
"""
usage_string = """\
phenix.python -m mmtbx.ions.svm.dump_sites model.pdb data.mtz [options ...]
Utility to dump information about the properties of water and ion sites in a
model. This properties include local environment, electron density maps, and
atomic properties.
"""
cmdline = load_model_and_data(
args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=True,
create_fmodel=True,
prefer_anomalous=True,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
usage_string=usage_string,
)
params = cmdline.params
params.use_svm = True
make_header("Inspecting sites", out=out)
manager = ions.identify.create_manager(
pdb_hierarchy=cmdline.pdb_hierarchy,
fmodel=cmdline.fmodel,
geometry_restraints_manager=cmdline.geometry,
wavelength=params.input.wavelength,
params=params,
verbose=params.debug,
nproc=params.nproc,
log=out,
)
manager.show_current_scattering_statistics(out=out)
sites = dump_sites(manager)
out_name = os.path.splitext(
params.input.pdb.file_name[0])[0] + "_sites.pkl"
print("Dumping to", out_name, file=out)
easy_pickle.dump(out_name, sites)
def _main(args, out=sys.stdout):
"""
Main entry point to this script.
Parameters
----------
args : list of str
List of arguments, should not include the first argument with the
executable name.
out : file, optional
"""
usage_string = """\
phenix.python -m mmtbx.ions.svm.dump_sites model.pdb data.mtz [options ...]
Utility to dump information about the properties of water and ion sites in a
model. This properties include local environment, electron density maps, and
atomic properties.
"""
cmdline = load_model_and_data(
args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=True,
create_fmodel=True,
prefer_anomalous=True,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
usage_string=usage_string,
)
params = cmdline.params
params.use_svm = True
make_header("Inspecting sites", out=out)
manager = ions.identify.create_manager(
pdb_hierarchy=cmdline.pdb_hierarchy,
fmodel=cmdline.fmodel,
geometry_restraints_manager=cmdline.geometry,
wavelength=params.input.wavelength,
params=params,
verbose=params.debug,
nproc=params.nproc,
log=out,
)
manager.show_current_scattering_statistics(out=out)
sites = dump_sites(manager)
out_name = os.path.splitext(params.input.pdb.file_name[0])[0] + "_sites.pkl"
print >> out, "Dumping to", out_name
easy_pickle.dump(out_name, sites)
def run (args, out=None) :
if (out is None) : out = sys.stdout
usage_string = """\
mmtbx.prune_model model.pdb data.mtz [options...]
Filters protein residues based on CC to 2mFo-DFc map and absolute
(sigma-scaled) values in 2mFo-DFc and mFo-DFc maps. For fast automatic
correction of MR solutions after initial refinement (ideally with rotamer
correction) to remove spurious loops and sidechains.
"""
from mmtbx.command_line import load_model_and_data
cmdline = load_model_and_data(
args=args,
master_phil=get_master_phil(),
out=out,
process_pdb_file=False,
create_fmodel=True)
params = cmdline.params
fmodel = cmdline.fmodel
if (params.output.file_name is None) :
base_name = os.path.basename(params.input.pdb.file_name[0])
params.output.file_name = os.path.splitext(base_name)[0] + "_pruned.pdb"
log_file = os.path.splitext(os.path.basename(params.output.file_name))[0] + \
".log"
log = open(log_file, "w")
out2 = multi_out()
out2.register("out", out)
out2.register("log", log)
map_helper = fmodel.electron_density_map()
f_map_coeffs = map_helper.map_coefficients(map_type="2mFo-DFc")
diff_map_coeffs = map_helper.map_coefficients(map_type="mFo-DFc")
model_map_coeffs = map_helper.map_coefficients(map_type="Fc")
result = prune_model(
f_map_coeffs=f_map_coeffs,
diff_map_coeffs=diff_map_coeffs,
model_map_coeffs=model_map_coeffs,
pdb_hierarchy=cmdline.pdb_hierarchy,
params=params.prune).process_residues(out=out2)
f = open(params.output.file_name, "w")
f.write("REMARK edited by mmtbx.prune_model\n")
f.write(cmdline.pdb_hierarchy.as_pdb_string(
crystal_symmetry=fmodel.xray_structure))
f.close()
log.close()
print >> out, "Wrote %s" % params.output.file_name
return params.output.file_name
def run(args, out=None):
if (out is None): out = sys.stdout
usage_string = """\
mmtbx.prune_model model.pdb data.mtz [options...]
Filters protein residues based on CC to 2mFo-DFc map and absolute
(sigma-scaled) values in 2mFo-DFc and mFo-DFc maps. For fast automatic
correction of MR solutions after initial refinement (ideally with rotamer
correction) to remove spurious loops and sidechains.
"""
from mmtbx.command_line import load_model_and_data
cmdline = load_model_and_data(args=args,
master_phil=get_master_phil(),
out=out,
process_pdb_file=False,
create_fmodel=True)
params = cmdline.params
fmodel = cmdline.fmodel
if (params.output.file_name is None):
base_name = os.path.basename(params.input.pdb.file_name[0])
params.output.file_name = os.path.splitext(
base_name)[0] + "_pruned.pdb"
log_file = os.path.splitext(os.path.basename(params.output.file_name))[0] + \
".log"
log = open(log_file, "w")
out2 = multi_out()
out2.register("out", out)
out2.register("log", log)
map_helper = fmodel.electron_density_map()
f_map_coeffs = map_helper.map_coefficients(map_type="2mFo-DFc")
diff_map_coeffs = map_helper.map_coefficients(map_type="mFo-DFc")
model_map_coeffs = map_helper.map_coefficients(map_type="Fc")
result = prune_model(f_map_coeffs=f_map_coeffs,
diff_map_coeffs=diff_map_coeffs,
model_map_coeffs=model_map_coeffs,
pdb_hierarchy=cmdline.pdb_hierarchy,
params=params.prune).process_residues(out=out2)
f = open(params.output.file_name, "w")
f.write("REMARK edited by mmtbx.prune_model\n")
f.write(
cmdline.pdb_hierarchy.as_pdb_string(
crystal_symmetry=fmodel.xray_structure))
f.close()
log.close()
print >> out, "Wrote %s" % params.output.file_name
return params.output.file_name
def run (args, out=sys.stdout) :
from mmtbx.command_line import load_model_and_data
import mmtbx.ncs.ligands
cmdline = load_model_and_data(
args=args,
master_phil=master_phil_str % mmtbx.ncs.ligands.ncs_ligand_phil,
out=out,
process_pdb_file=True,
generate_input_phil=True,
usage_string="""\
mmtbx.apply_ncs_to_ligand model.pdb data.mtz ligand_code=LIG ...
Given a multi-chain PDB file and a ligand residue name, find copies of the
ligand in the input file, identify NCS operators relating macromolecule chains,
and search for additional ligand sites by applying these operators. Used to
complete ligand placement in cases where LigandFit (etc.) is only partially
successful.
""")
pdb_hierarchy = cmdline.pdb_hierarchy
fmodel = cmdline.fmodel
params = cmdline.params
if (params.output_file is None) :
params.output_file = "ncs_ligands.pdb"
if (params.output_map is None) :
params.output_map = "ncs_ligands.mtz"
make_header("Finding ligands by NCS operators", out=out)
result = mmtbx.ncs.ligands.apply_ligand_ncs(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
params=params,
ligand_code=params.ligand_code,
atom_selection=None,
add_new_ligands_to_pdb=params.add_to_model,
log=out)
result.write_pdb(params.output_file)
result.write_maps(params.output_map)
return result
def run (args, out=sys.stdout) :
usage_string = """\
mmtbx.show_suspicious_residues [model] [data] [options...]
Flag bad residues based on fit to electron density. By default, only HETATM
records will be inspected.
"""
from mmtbx import real_space_correlation
from mmtbx.command_line import load_model_and_data
cmdline = load_model_and_data(
args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=False,
usage_string=usage_string)
params = cmdline.params
ignore_list = []
if (params.skip_xtal_solution_mols) :
ignore_list = common_xtal_mols
outliers = real_space_correlation.find_suspicious_residues(
fmodel=cmdline.fmodel,
pdb_hierarchy=cmdline.pdb_hierarchy,
hetatms_only=params.hetatms_only,
skip_single_atoms=params.skip_single_atoms,
skip_alt_confs=params.skip_alt_confs,
ignore_resnames=ignore_list,
min_acceptable_cc=params.min_acceptable_cc,
min_acceptable_2fofc=params.min_acceptable_2fofc,
max_frac_atoms_below_min=params.max_frac_atoms_below_min,
log=out)
map_file = None
if ((params.write_maps == True) or
((len(outliers) > 0) and (params.write_maps in [Auto, True]))) :
import mmtbx.maps.utils
import iotbx.map_tools
f_map, diff_map = mmtbx.maps.utils.get_maps_from_fmodel(cmdline.fmodel)
anom_map = None
if (cmdline.fmodel.f_obs().anomalous_flag()) :
anom_map = mmtbx.maps.utils.get_anomalous_map(cmdline.fmodel)
base_name = os.path.basename(
os.path.splitext(params.input.xray_data.file_name)[0])
map_file = base_name + "_maps.mtz"
iotbx.map_tools.write_map_coeffs(
fwt_coeffs=f_map,
delfwt_coeffs=diff_map,
file_name=map_file,
anom_coeffs=anom_map)
print "Wrote maps to %s" % map_file
if (len(outliers) > 0) and (params.write_coot_script) :
zoom_list_base = libtbx.env.find_in_repositories(
relative_path="cctbx_project/cootbx/simple_zoom_list.py",
test=os.path.isfile)
script = open("coot_bad_residues.py", "w")
script.write(open(zoom_list_base).read())
script.write("\n")
for file_name in params.input.pdb.file_name :
script.write("""read_pdb("%s")\n""" % file_name)
if (map_file is not None) :
script.write("auto_read_make_and_draw_maps(\"%s\")\n" % map_file)
script.write("""
draw_simple_zoom_list(
title="Residues in suspicious density",
items=%s)
""" % str(outliers))
script.close()
print "Coot script is coot_bad_residues.py"
def run(args, out=sys.stdout):
usage_string = """\
mmtbx.show_suspicious_residues [model] [data] [options...]
Flag bad residues based on fit to electron density. By default, only HETATM
records will be inspected.
"""
from mmtbx import real_space_correlation
from mmtbx.command_line import load_model_and_data
cmdline = load_model_and_data(args=args,
master_phil=master_phil(),
out=out,
process_pdb_file=False,
usage_string=usage_string)
params = cmdline.params
ignore_list = []
if (params.skip_xtal_solution_mols):
ignore_list = common_xtal_mols
outliers = real_space_correlation.find_suspicious_residues(
fmodel=cmdline.fmodel,
pdb_hierarchy=cmdline.pdb_hierarchy,
hetatms_only=params.hetatms_only,
skip_single_atoms=params.skip_single_atoms,
skip_alt_confs=params.skip_alt_confs,
ignore_resnames=ignore_list,
min_acceptable_cc=params.min_acceptable_cc,
min_acceptable_2fofc=params.min_acceptable_2fofc,
max_frac_atoms_below_min=params.max_frac_atoms_below_min,
log=out)
map_file = None
if ((params.write_maps == True)
or ((len(outliers) > 0) and (params.write_maps in [Auto, True]))):
import mmtbx.maps.utils
import iotbx.map_tools
f_map, diff_map = mmtbx.maps.utils.get_maps_from_fmodel(cmdline.fmodel)
anom_map = None
if (cmdline.fmodel.f_obs().anomalous_flag()):
anom_map = mmtbx.maps.utils.get_anomalous_map(cmdline.fmodel)
base_name = os.path.basename(
os.path.splitext(params.input.xray_data.file_name)[0])
map_file = base_name + "_maps.mtz"
iotbx.map_tools.write_map_coeffs(fwt_coeffs=f_map,
delfwt_coeffs=diff_map,
file_name=map_file,
anom_coeffs=anom_map)
print "Wrote maps to %s" % map_file
if (len(outliers) > 0) and (params.write_coot_script):
zoom_list_base = libtbx.env.find_in_repositories(
relative_path="cctbx_project/cootbx/simple_zoom_list.py",
test=os.path.isfile)
script = open("coot_bad_residues.py", "w")
script.write(open(zoom_list_base).read())
script.write("\n")
for file_name in params.input.pdb.file_name:
script.write("""read_pdb("%s")\n""" % file_name)
if (map_file is not None):
script.write("auto_read_make_and_draw_maps(\"%s\")\n" % map_file)
script.write("""
draw_simple_zoom_list(
title="Residues in suspicious density",
items=%s)
""" % str(outliers))
script.close()
print "Coot script is coot_bad_residues.py"