def run (args, out=sys.stdout) :
from libtbx.utils import Usage
if (len(args) == 0) :
print "Warning: this is not intended for general use."
raise Usage("mmtbx.flip_peptides [model.pdb] [data.mtz] [params ...]")
from mmtbx.refinement import flip_peptides, print_statistics
import mmtbx.command_line
master_phil = mmtbx.command_line.generate_master_phil_with_inputs(
enable_automatic_twin_detection=True,
phil_string="""
flip_peptides {
include scope mmtbx.refinement.flip_peptides.master_params_str
}""")
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_phil,
out=out)
print >> out, ""
print_statistics.make_header("Analyzing peptide bonds", out=out)
fmodel = cmdline.fmodel
flip_peptides.run(
fmodel=fmodel,
geometry_restraints_manager=cmdline.geometry,
pdb_hierarchy=cmdline.pdb_hierarchy,
solvent_selection=None,
params=cmdline.params.flip_peptides)
if (len(cmdline.params.input.pdb.file_name) == 1) :
pdb_file = cmdline.params.input.pdb.file_name[0]
pdb_out = os.path.splitext(os.path.basename(pdb_file))[0] + "_new.pdb"
else :
pdb_out = "flipped.pdb"
open(pdb_out, "w").write(cmdline.pdb_hierarchy.as_pdb_string())
print >> out, ""
print "wrote new PDB file to %s" % pdb_out
def build_dod_and_od(model, fmodels, log=None, params=None):
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc = True,
update_f_mask = True)
fmodels.show_short()
hbparams = params.hydrogens.build
if hbparams is None:
hbparams = all_master_params().extract()
if log is None:
log = fmodels.log
if fmodels.fmodel_n is not None:
fmodel = fmodels.fmodel_neutron()
else:
fmodel = fmodels.fmodel_xray()
title = "xray"
if fmodel.xray_structure.guess_scattering_type_neutron():
title="neutron"
print_statistics.make_header("Build water hydrogens into "+title+" difference"
" map", out=log)
model = build_water_hydrogens_from_map2(model, fmodel, params=hbparams, log=log)
#
if hbparams.filter_dod:
bmax=params.ordered_solvent.b_iso_max
water_map_correlations(model, fmodels, log)
model = remove_zero_occupancy(model,0.01,bmax)
model.reprocess_pdb_hierarchy_inefficient()
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc = True,
update_f_mask = True)
fmodels.show_short()
mmtbx.utils.assert_model_is_consistent(model)
sol_sel = model.solvent_selection()
hd_sel = sol_sel & model.xray_structure.hd_selection()
print>>log, "Final number of water hydrogens: ", hd_sel.count(True)
return model, fmodels
def run(fmodel, model, log, params = None):
print_statistics.make_header("Fit water hydrogens into residual map",
out = log)
if(params is None):
params = all_master_params().extract()
print_statistics.make_sub_header("find peak-candidates", out = log)
peaks = find_hydrogen_peaks(
fmodel = fmodel,
pdb_atoms = model.pdb_atoms,
params = params,
log = log)
waters_and_peaks = extract_hoh_peaks(
peaks = peaks,
pdb_hierarchy = model.pdb_hierarchy(),
pdb_atoms = model.pdb_atoms,
xray_structure = model.xray_structure)
print_statistics.make_sub_header("6D rigid body fit of HOH", out = log)
print >> log, "Fit quality:"
for water_and_peaks in waters_and_peaks:
fit_water(water_and_peaks = water_and_peaks,
xray_structure = model.xray_structure,
params = params,
log = log)
# adjust ADP for H
# TODO mrt: probably H bfactors should be equal to those
# of the bonded atom
u_isos = model.xray_structure.extract_u_iso_or_u_equiv()
u_iso_mean = flex.mean(u_isos)
sel_big = u_isos > u_iso_mean*2
hd_sel = model.xray_structure.hd_selection()
sel_big.set_selected(~hd_sel, False)
model.xray_structure.set_u_iso(value = u_iso_mean, selection = sel_big)
def run(args=(),
params=None,
pdb_hierarchy=None,
xray_structure=None,
out=None):
if (out is None):
out = sys.stdout
print_statistics.make_header("phenix.find_tls_groups", out=out)
default_message = """\
phenix.find_tls_groups: Tool for automated partitioning a model into TLS groups.
Usage:
phenix.find_tls_groups model.pdb [nproc=...]
"""
if (len(args) == 0):
print(default_message)
return
cmdline_phil = []
for arg in args:
if os.path.isfile(arg):
if iotbx.pdb.is_pdb_file(arg) or iotbx.pdb.is_pdb_mmcif_file(arg):
pdb_phil = libtbx.phil.parse("pdb_file=%s" %
os.path.abspath(arg))
cmdline_phil.append(pdb_phil)
else:
try:
file_phil = libtbx.phil.parse(file_name=arg)
except Exception:
raise Sorry("Bad parameter file: %s" % arg)
cmdline_phil.append(file_phil)
else:
try:
arg_phil = libtbx.phil.parse(arg)
except Exception:
raise Sorry("Bad parameter: %s" % arg)
cmdline_phil.append(arg_phil)
working_phil = master_phil.fetch(sources=cmdline_phil)
params = working_phil.extract()
# XXX params.pdb_file is not used anymore. Maybe should be removed.
pdb_file_name = params.pdb_file
if ((pdb_file_name is None)
or (not iotbx.pdb.is_pdb_file(pdb_file_name)
and not iotbx.pdb.is_pdb_mmcif_file(pdb_file_name))):
print("A model file is required.")
return
if (params.nproc is None):
params.nproc = 1
pdb_inp = iotbx.pdb.input(file_name=pdb_file_name)
pdb_hierarchy = pdb_inp.construct_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
#
xray_structure = pdb_inp.xray_structure_simple()
return find_tls(
params=params,
# pdb_inp = pdb_inp,
pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
out=out)
def run(fmodel, model, log, params=None):
print_statistics.make_header("Fit water hydrogens into residual map",
out=log)
if (params is None):
params = all_master_params().extract()
print_statistics.make_sub_header("find peak-candidates", out=log)
peaks = find_hydrogen_peaks(fmodel=fmodel,
pdb_atoms=model.get_atoms(),
params=params,
log=log)
waters_and_peaks = extract_hoh_peaks(
peaks=peaks,
pdb_hierarchy=model.get_hierarchy(),
pdb_atoms=model.get_atoms(),
xray_structure=model.get_xray_structure())
print_statistics.make_sub_header("6D rigid body fit of HOH", out=log)
print("Fit quality:", file=log)
for water_and_peaks in waters_and_peaks:
fit_water(water_and_peaks=water_and_peaks,
xray_structure=model.get_xray_structure(),
params=params,
log=log)
# adjust ADP for H
# TODO mrt: probably H bfactors should be equal to those
# of the bonded atom
u_isos = model.get_xray_structure().extract_u_iso_or_u_equiv()
u_iso_mean = flex.mean(u_isos)
sel_big = u_isos > u_iso_mean * 2
hd_sel = model.get_hd_selection()
sel_big.set_selected(~hd_sel, False)
model.get_xray_structure().set_u_iso(value=u_iso_mean, selection=sel_big)
def update_all_scales(self,
update_f_part1,
remove_outliers=True,
params=None,
optimize_mask=False,
force_update_f_mask=False,
nproc=1,
log=None,
apply_back_trace=False,
refine_hd_scattering=None):
"""
...
"""
if log is None: log = self.log
fast = True
if (params.mode == "slow"): fast = False
from mmtbx.refinement import print_statistics
print_statistics.make_header("updating all scales", out=log)
self.update_xray_structure(update_f_calc=True,
update_f_mask=True,
force_update_f_mask=force_update_f_mask)
if ([self.fmodel_x, self.fmodel_n].count(None) == 0):
apply_back_trace = False
if (self.fmodel_x is not None):
msg = None
if (self.fmodel_n is not None):
msg = "X-ray:"
print >> log, msg
self.fmodel_xray().update_all_scales(
update_f_part1=update_f_part1,
remove_outliers=remove_outliers,
params=params,
fast=fast,
log=log,
show=True,
optimize_mask=optimize_mask,
nproc=nproc,
apply_back_trace=apply_back_trace,
refine_hd_scattering=refine_hd_scattering)
self.fmodel_x.show(log=log, suffix=msg)
if (self.fmodel_n is not None):
msg = "Neutron:"
print >> log, msg
self.fmodel_neutron().update_all_scales(
update_f_part1=update_f_part1,
remove_outliers=remove_outliers,
params=params,
fast=fast,
log=log,
show=True,
optimize_mask=optimize_mask,
nproc=nproc,
apply_back_trace=apply_back_trace,
refine_hd_scattering=refine_hd_scattering)
self.fmodel_n.show(log=log, suffix=msg)
def update_all_scales(
self,
update_f_part1,
remove_outliers = True,
params = None,
optimize_mask = False,
force_update_f_mask = False,
nproc = 1,
log = None,
apply_back_trace = False,
refine_hd_scattering=None):
"""
...
"""
if log is None: log = self.log
fast=True
if(params.mode=="slow"): fast=False
from mmtbx.refinement import print_statistics
print_statistics.make_header("updating all scales", out = log)
self.update_xray_structure(update_f_calc = True, update_f_mask = True,
force_update_f_mask = force_update_f_mask)
if([self.fmodel_x, self.fmodel_n].count(None)==0): apply_back_trace=False
if(self.fmodel_x is not None):
msg = None
if(self.fmodel_n is not None):
msg = "X-ray:"
print >> log, msg
self.fmodel_xray().update_all_scales(
update_f_part1 = update_f_part1,
remove_outliers = remove_outliers,
params = params,
fast = fast,
log = log,
show = True,
optimize_mask = optimize_mask,
nproc = nproc,
apply_back_trace = apply_back_trace,
refine_hd_scattering = refine_hd_scattering)
self.fmodel_x.show(log = log, suffix = msg)
if(self.fmodel_n is not None):
msg = "Neutron:"
print >> log, msg
self.fmodel_neutron().update_all_scales(
update_f_part1 = update_f_part1,
remove_outliers = remove_outliers,
params = params,
fast = fast,
log = log,
show = True,
optimize_mask = optimize_mask,
nproc = nproc,
apply_back_trace = apply_back_trace,
refine_hd_scattering = refine_hd_scattering)
self.fmodel_n.show(log = log, suffix = msg)
def run(args,
crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if (log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message = """\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:""" % h
if (len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
# Process inputs ignoring symmetry conflicts just to get the value of
# ignore_symmetry_conflicts...
inputs = mmtbx.utils.process_command_line_args(
args=args,
cmd_cs=crystal_symmetry,
master_params=master_phil,
suppress_symmetry_related_errors=True)
params = inputs.params.extract()
# Now process inputs for real and write a nice error message if necessary.
try:
inputs = mmtbx.utils.process_command_line_args(
args=args,
cmd_cs=crystal_symmetry,
master_params=master_phil,
suppress_symmetry_related_errors=params.ignore_symmetry_conflicts)
except Exception, e:
if str(e).find("symmetry mismatch ") > 1:
raise Sorry(str(e) + "\nTry 'ignore_symmetry_conflicts=True'")
else:
raise e
def manager(params,
target_weights,
all_params,
macro_cycle,
h_params,
fmodels,
model,
out=None,
states_collector=None,
callback=None):
if (out is None): out = sys.stdout
if (states_collector is not None):
assert hasattr(states_collector, "add")
print_statistics.make_header("simulated annealing refinement", out=out)
model.set_refine_individual_sites()
fmodel = fmodels.fmodel_xray() # XXX use only xray data
fmodel.xray_structure = model.get_xray_structure(
) # XXX use only xray data
if (params.max_number_of_iterations >= 0):
print_statistics.make_sub_header(
"lbfgs minimization: before simulated annealing", out=out)
is_neutron_scat_table = False
if (all_params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
import scitbx.lbfgs
minimized = mmtbx.refinement.minimization.lbfgs(
restraints_manager=model.restraints_manager,
refine_xyz=True,
fmodels=fmodels,
is_neutron_scat_table=is_neutron_scat_table,
model=model,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=params.max_number_of_iterations),
target_weights=target_weights,
h_params=h_params,
verbose=0)
fmodel.update_xray_structure(xray_structure=model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
print_statistics.make_header("simulated annealing", out=out)
wx = target_weights.xyz_weights_result.wx * \
target_weights.xyz_weights_result.wx_scale
run(params=params,
restraints_manager=model.restraints_manager,
fmodel=fmodel,
wx=wx,
wc=target_weights.xyz_weights_result.w,
states_collector=states_collector,
callback=callback,
log=out)
def manager(params,
target_weights,
all_params,
macro_cycle,
h_params,
fmodels,
model,
out = None,
states_collector=None,
callback=None):
if(out is None): out = sys.stdout
if (states_collector is not None) :
assert hasattr(states_collector, "add")
print_statistics.make_header("simulated annealing refinement", out = out)
model.set_refine_individual_sites()
fmodel = fmodels.fmodel_xray() # XXX use only xray data
fmodel.xray_structure = model.xray_structure # XXX use only xray data
if (params.max_number_of_iterations >= 0):
print_statistics.make_sub_header(
"lbfgs minimization: before simulated annealing", out = out)
is_neutron_scat_table = False
if(all_params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
import scitbx.lbfgs
minimized = mmtbx.refinement.minimization.lbfgs(
restraints_manager = model.restraints_manager,
refine_xyz = True,
fmodels = fmodels,
is_neutron_scat_table = is_neutron_scat_table,
model = model,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = params.max_number_of_iterations),
target_weights = target_weights,
h_params = h_params,
verbose = 0)
fmodel.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc = True,
update_f_mask = True)
print_statistics.make_header("simulated annealing", out = out)
wx = target_weights.xyz_weights_result.wx * \
target_weights.xyz_weights_result.wx_scale
run(
params = params,
restraints_manager = model.restraints_manager,
fmodel = fmodel,
wx = wx,
wc = target_weights.xyz_weights_result.w,
states_collector = states_collector,
callback = callback,
log = out)
def run (args=(), params=None, pdb_hierarchy=None, xray_structure=None,
out=None) :
if (out is None) :
out = sys.stdout
print_statistics.make_header("phenix.find_tls_groups", out=out)
default_message="""\
phenix.find_tls_groups: Tool for automated partitioning a model into TLS groups.
Usage:
phenix.find_tls_groups model.pdb [nproc=...]
"""
if(len(args) == 0):
print default_message
return
cmdline_phil = []
for arg in args :
if os.path.isfile(arg):
if iotbx.pdb.is_pdb_file(arg):
pdb_phil = libtbx.phil.parse("pdb_file=%s" % os.path.abspath(arg))
cmdline_phil.append(pdb_phil)
else:
try: file_phil = libtbx.phil.parse(file_name=arg)
except Exception: raise Sorry("Bad parameter file: %s"%arg)
cmdline_phil.append(file_phil)
else:
try: arg_phil = libtbx.phil.parse(arg)
except Exception: raise Sorry("Bad parameter: %s"%arg)
cmdline_phil.append(arg_phil)
working_phil = master_phil.fetch(sources=cmdline_phil)
params = working_phil.extract()
pdb_file_name = params.pdb_file
if (pdb_file_name is None) or (not iotbx.pdb.is_pdb_file(pdb_file_name)) :
print "A model file is required."
return
if (params.nproc is None) :
params.nproc = 1
pdb_inp = iotbx.pdb.input(file_name=pdb_file_name)
pdb_hierarchy = pdb_inp.construct_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
#
xray_structure = pdb_inp.xray_structure_simple()
return find_tls(
params = params,
pdb_inp = pdb_inp,
pdb_hierarchy = pdb_hierarchy,
xray_structure = xray_structure,
out = out)
def updaterdl(self, prefix):
if self.restraints_manager is None: return
from mmtbx.conformation_dependent_library import rotamers
from mmtbx.refinement import print_statistics
print_statistics.make_header(prefix, out=self.log)
self.rdl_proxies = None #rotamers.setup_restraints(result)
rc = rotamers.update_restraints(
self.pdb_hierarchy,
self.restraints_manager.geometry,
current_geometry=self.pdb_hierarchy.extract_xray_structure(),
rdl_proxies=self.rdl_proxies,
log=self.log,
verbose=False,
)
print >> self.log, "=" * 79
return rc
def updaterdl(self, prefix):
if self.restraints_manager is None: return
from mmtbx.conformation_dependent_library import rotamers
from mmtbx.refinement import print_statistics
print_statistics.make_header(prefix, out=self.log)
self.rdl_proxies = None #rotamers.setup_restraints(result)
rc = rotamers.update_restraints(
self.pdb_hierarchy,
self.restraints_manager.geometry,
current_geometry=self.pdb_hierarchy.extract_xray_structure(),
rdl_proxies=self.rdl_proxies,
log=self.log,
verbose=False,
)
print >> self.log, "="*79
return rc
def external_tls(pdb_inp, pdb_hierarchy, sites_cart, u_iso, out=None):
if (out is None):
out = sys.stdout
pdb_inp_tls = pdb_inp.extract_tls_params(pdb_hierarchy)
print_statistics.make_header("TLS groups from PDB file header", out=out)
selection_strings = []
if (len(pdb_inp_tls.tls_params) > 0):
for tp in pdb_inp_tls.tls_params:
print >> out, " ", tp.selection_string
selection_strings.append(tp.selection_string)
else:
print >> out, " ... none found."
if (len(selection_strings) > 0):
total_target = total_score(pdb_hierarchy=pdb_hierarchy,
sites_cart=sites_cart,
u_iso=u_iso,
selection_strings=selection_strings)
print >> out
print >> out, "Total target for groups from PDB file header: %10.1f" % total_target
def water_map_correlations(model, fmodels, log=None):
print_statistics.make_header("Water real space correlations", out=log)
fmodels.update_xray_structure(xray_structure=model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
fmodels.show_short()
scatterers = model.get_xray_structure().scatterers()
waters = model.solvent_selection()
water_rgs = model.extract_water_residue_groups()
n_atoms = len(scatterers)
for rg in water_rgs:
o_atom = get_pdb_oxygen(rg)
o_scat = scatterers[o_atom.i_seq]
water = select_one_water(rg, n_atoms)
if water.count(True) < 2:
continue
for s, u in zip(scatterers, water):
if u:
e = s.element_symbol().strip()
if e == 'D':
if s.occupancy <= 0.02 or s.occupancy >= 0.98:
keep_occ = s.occupancy
neutron_cc = one_water_correlation(
model, fmodels, water)
if s.occupancy <= 0.02:
s.occupancy = 1.0
s.u_iso = o_scat.u_iso
else:
s.occupancy = 0.0
fmodels.update_xray_structure(
xray_structure=model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
ncc = one_water_correlation(model, fmodels, water)
if ncc < neutron_cc:
s.occupancy = keep_occ
fmodels.update_xray_structure(
xray_structure=model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
else:
neutron_cc = ncc
return True
def show_den_opt_summary_cartesian(self, grid_results):
print_statistics.make_header(
"DEN Cartesian weight optimization results", out=self.log)
print >>self.log,"|---------------------------------------"+\
"--------------------------------------|"
print >>self.log,"| Gamma Weight R-free "+\
" |"
for result in grid_results:
if result == None:
raise RuntimeError("Parallel DEN job failed: %s" % str(out))
cur_gamma = result[0]
cur_weight = result[1]
cur_r_free = result[2]
print >> self.log, "| %6.1f %6.1f %6.4f " %\
(cur_gamma,
cur_weight,
cur_r_free)+\
" |"
print >>self.log,"|---------------------------------------"+\
"--------------------------------------|"
def summarize_contacts_by_residue(residue_contacts,
pdb_hierarchy,
out=sys.stdout):
from mmtbx.refinement.print_statistics import make_header
summary = extract_closest_contacting_residues(residue_contacts,
pdb_hierarchy.atoms())
make_header("Crystal contacts by residue", out=out)
print >> out, " %-16s %-16s %-16s %-16s" % ("residue", "closest contact",
"symop", "distance (A)")
print >> out, "-" * 72
for (residue_key, contact_key, sym_op, distance) in summary:
(chain_id, resname, resid, altloc) = residue_key
id_str = "%s%5s %3s %s" % (chain_id, resid, resname, altloc)
if (contact_key is None):
print >> out, " %-16s %-16s %-16s %-4s" % (id_str, "*", "*", "*")
else:
(chain_id, resname, resid, altloc) = contact_key
id_str_2 = "%s%5s %3s %s" % (chain_id, resid, resname, altloc)
print >> out, " %-16s %-16s %-16s %-4.2f" % (id_str, id_str_2,
sym_op, distance)
def summarize_contacts_by_residue (residue_contacts,
pdb_hierarchy,
out=sys.stdout) :
from mmtbx.refinement.print_statistics import make_header
summary = extract_closest_contacting_residues(residue_contacts,
pdb_hierarchy.atoms())
make_header("Crystal contacts by residue", out=out)
print >> out, " %-16s %-16s %-16s %-16s" % ("residue", "closest contact",
"symop", "distance (A)")
print >> out, "-"*72
for (residue_key, contact_key, sym_op, distance) in summary :
(chain_id, resname, resid, altloc) = residue_key
id_str = "%s%5s %3s %s" % (chain_id, resid, resname, altloc)
if (contact_key is None) :
print >> out, " %-16s %-16s %-16s %-4s" % (id_str, "*","*","*")
else :
(chain_id, resname, resid, altloc) = contact_key
id_str_2 = "%s%5s %3s %s" % (chain_id, resid, resname, altloc)
print >> out, " %-16s %-16s %-16s %-4.2f" % (id_str, id_str_2, sym_op,
distance)
def show_den_opt_summary_cartesian(self, grid_results):
print_statistics.make_header(
"DEN Cartesian weight optimization results", out=self.log)
print >>self.log,"|---------------------------------------"+\
"--------------------------------------|"
print >>self.log,"| Gamma Weight R-free "+\
" |"
for result in grid_results:
if result == None:
raise RuntimeError("Parallel DEN job failed: %s" % str(out))
cur_gamma = result[0]
cur_weight = result[1]
cur_r_free = result[2]
print >> self.log, "| %6.1f %6.1f %6.4f " %\
(cur_gamma,
cur_weight,
cur_r_free)+\
" |"
print >>self.log,"|---------------------------------------"+\
"--------------------------------------|"
def external_tls(pdb_inp, pdb_hierarchy, sites_cart, u_iso, out=None) :
if (out is None) :
out = sys.stdout
pdb_inp_tls = pdb_inp.extract_tls_params(pdb_hierarchy)
print_statistics.make_header("TLS groups from PDB file header",
out = out)
selection_strings = []
if(len(pdb_inp_tls.tls_params)>0):
for tp in pdb_inp_tls.tls_params:
print >> out, " ", tp.selection_string
selection_strings.append(tp.selection_string)
else:
print >> out, " ... none found."
if(len(selection_strings)>0):
total_target = total_score(
pdb_hierarchy = pdb_hierarchy,
sites_cart = sites_cart,
u_iso = u_iso,
selection_strings = selection_strings)
print >> out
print >> out, "Total target for groups from PDB file header: %10.1f"%total_target
def build_dod_and_od(model, fmodels, log=None, params=None):
fmodels.update_xray_structure(xray_structure=model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
fmodels.show_short()
hbparams = params.hydrogens.build
if hbparams is None:
hbparams = all_master_params().extract()
if log is None:
log = fmodels.log
if fmodels.fmodel_n is not None:
fmodel = fmodels.fmodel_neutron()
else:
fmodel = fmodels.fmodel_xray()
title = "xray"
if fmodel.xray_structure.guess_scattering_type_neutron():
title = "neutron"
print_statistics.make_header("Build water hydrogens into " + title +
" difference"
" map",
out=log)
model = build_water_hydrogens_from_map2(model,
fmodel,
params=hbparams,
log=log)
#
if hbparams.filter_dod:
bmax = params.ordered_solvent.b_iso_max
water_map_correlations(model, fmodels, log)
model = remove_zero_occupancy(model, 0.01, bmax)
model.reprocess_pdb_hierarchy_inefficient()
fmodels.update_xray_structure(xray_structure=model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
fmodels.show_short()
mmtbx.utils.assert_model_is_consistent(model)
sol_sel = model.solvent_selection()
hd_sel = sol_sel & model.get_hd_selection()
print("Final number of water hydrogens: ", hd_sel.count(True), file=log)
return model, fmodels
def refine_adp_for_h_only(fmodels, model, params, prefix, log):
print_statistics.make_header(prefix, out = log)
xrs_start = model.xray_structure.deep_copy_scatterers()
fmodels.show_targets(log = log, text = "start")
fmodels.fmodel_xray().xray_structure.scatterers().flags_set_grads(
state = False)
i_selection = model.xray_structure.hd_selection().iselection()
fmodels.fmodel_xray().xray_structure.scatterers(
).flags_set_grad_u_iso(iselection = i_selection)
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = params.main.max_number_of_iterations)
is_neutron_scat_table = False
if(params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
minimized = mmtbx.refinement.minimization.lbfgs(
restraints_manager = None,
is_neutron_scat_table = is_neutron_scat_table,
fmodels = fmodels,
model = model,
refine_adp = True,
lbfgs_termination_params = lbfgs_termination_params)
fmodels.show_targets(log = log, text = "final")
def refine_adp_for_ias_only(fmodels, model, params, prefix, log):
print_statistics.make_header(prefix, out = log)
xrs_start = model.xray_structure.deep_copy_scatterers()
fmodels.show_targets(log = log, text = "start")
fmodels.fmodel_xray().xray_structure.scatterers().flags_set_grads(
state = False)
i_selection = model.ias_selection.iselection()
scatterers = fmodels.fmodel_xray().xray_structure.scatterers()
for i_sel in i_selection:
if(scatterers[i_sel].flags.use_u_iso()):
scatterers[i_sel].flags.set_grad_u_iso(True)
if(scatterers[i_sel].flags.use_u_aniso()):
scatterers[i_sel].flags.set_grad_u_aniso(True)
#
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = params.main.max_number_of_iterations)
minimized = mmtbx.refinement.minimization.lbfgs(
restraints_manager = None,
fmodels = fmodels,
model = model,
refine_adp = True,
lbfgs_termination_params = lbfgs_termination_params)
fmodels.show_targets(log = log, text = "final")
def show_highest_peaks_and_deepest_holes(fmodel,
pdb_atoms,
map_type,
map_cutoff_plus,
map_cutoff_minus,
log=None):
if (log is None): log = sys.stdout
print_statistics.make_header(
"residual map %s: highest peaks and deepst holes" % map_type, out=log)
fp_params = master_params.extract()
fp_params.map_next_to_model.min_model_peak_dist = 0.7
fp_params.map_next_to_model.min_peak_peak_dist = 0.7
fp_params.peak_search.min_cross_distance = 0.7
fp_params.map_next_to_model.use_hydrogens = True
for par in [(map_cutoff_plus, "peaks"), (map_cutoff_minus, "holes")]:
print_statistics.make_sub_header(par[1], out=log)
result = manager(fmodel=fmodel,
map_type="mFobs-DFmodel",
map_cutoff=par[0],
params=fp_params,
log=log)
result.peaks_mapped()
result.show_mapped(pdb_atoms=pdb_atoms)
def show_highest_peaks_and_deepest_holes(fmodel,
pdb_atoms,
map_type,
map_cutoff_plus,
map_cutoff_minus,
log = None):
if(log is None): log = sys.stdout
print_statistics.make_header(
"residual map %s: highest peaks and deepst holes"%map_type, out = log)
fp_params = master_params.extract()
fp_params.map_next_to_model.min_model_peak_dist = 0.7
fp_params.map_next_to_model.min_peak_peak_dist = 0.7
fp_params.peak_search.min_cross_distance = 0.7
fp_params.map_next_to_model.use_hydrogens = True
for par in [(map_cutoff_plus,"peaks"), (map_cutoff_minus,"holes")]:
print_statistics.make_sub_header(par[1], out = log)
result = manager(fmodel = fmodel,
map_type = "mFobs-DFmodel",
map_cutoff = par[0],
params = fp_params,
log = log)
result.peaks_mapped()
result.show_mapped(pdb_atoms = pdb_atoms)
def water_map_correlations(model, fmodels, log=None):
print_statistics.make_header("Water real space correlations", out=log)
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc=True, update_f_mask=True)
fmodels.show_short()
scatterers = model.xray_structure.scatterers()
waters = model.solvent_selection()
water_rgs = model.extract_water_residue_groups()
n_atoms = len(scatterers)
for rg in water_rgs:
o_atom = get_pdb_oxygen(rg)
o_scat = scatterers[o_atom.i_seq]
water = select_one_water(rg, n_atoms)
if water.count(True) < 2:
continue
for s,u in zip(scatterers,water):
if u:
e = s.element_symbol().strip()
if e=='D':
if s.occupancy <= 0.02 or s.occupancy >=0.98:
keep_occ = s.occupancy
neutron_cc = one_water_correlation(model, fmodels, water)
if s.occupancy <= 0.02:
s.occupancy = 1.0
s.u_iso = o_scat.u_iso
else:
s.occupancy = 0.0
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc=True, update_f_mask=True)
ncc = one_water_correlation(model, fmodels, water)
if ncc < neutron_cc:
s.occupancy = keep_occ
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc=True, update_f_mask=True)
else:
neutron_cc = ncc
return True
def run(args,
crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if (log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message = """\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:""" % h
if (len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args=args,
cmd_cs=crystal_symmetry,
master_params=master_phil)
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds = lower_bounds
if upper_bounds:
params.upper_bounds = upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names = [params.pdb_file]
if (len(inputs.pdb_file_names) != 1 and not params.density_select
and not pdb_hierarchy and not params.keep_map_size
and not params.upper_bounds and not params.extract_unique):
raise Sorry("PDB file is needed unless extract_unique, " +
"density_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms or params.soft_mask )):
raise Sorry("PDB file is needed for mask_atoms or soft_mask")
if (params.density_select and params.keep_map_size):
raise Sorry("Cannot set both density_select and keep_map_size")
if (params.density_select and params.upper_bounds):
raise Sorry("Cannot set both density_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique and not params.resolution):
raise Sorry("Please set resolution for extract_unique")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names) > 0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy = None
# Map or map coefficients
map_coeff = None
if (not map_data):
# read first mtz file
if ((len(inputs.reflection_file_names) > 0)
or (params.map_coefficients_file is not None)):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(
params.map_coefficients_file)
else:
inputs.reflection_file_names[
0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name=inputs.reflection_file_names[0],
label=params.label,
type="complex",
log=log)
if not crystal_symmetry:
crystal_symmetry = map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(
resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix = os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ((inputs.ccp4_map is not None)
or (params.ccp4_map_file is not None)):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ", out=log)
if not crystal_symmetry:
crystal_symmetry = ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix = None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry = crystal_symmetry
# final check that map_data exists
if (map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names) > 0:
output_prefix = os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix = map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy = iotbx.pdb.input(
source_info='', lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string=params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'" % params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(radius=params.selection_radius,
selection=selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file, log=log)
print >> log, "Total of %s operators read" % (
ncs_object.max_operators())
if not ncs_object or ncs_object.max_operators() < 1:
print >> log, "No symmetry available"
if ncs_object:
n_ops = max(1, ncs_object.max_operators())
else:
n_ops = 1
# Get sequence if extract_unique is set
sequence = None
if params.extract_unique:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence and multiply
remove_duplicates = True
else:
remove_duplicates = False
from iotbx.bioinformatics import get_sequences
sequence = n_ops * (" ".join(
get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None, 'PROTEIN']:
n_protein = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='PROTEIN'))
else:
n_protein = 0
if params.chain_type in [None, 'RNA']:
n_rna = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='RNA'))
else:
n_rna = 0
if params.chain_type in [None, 'DNA']:
n_dna = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='DNA'))
else:
n_dna = 0
params.molecular_mass = n_protein * 110 + (n_rna + n_dna) * 330
elif not params.molecular_mass:
raise Sorry(
"Need a sequence file or molecular mass for extract_unique")
else:
molecular_mass = None
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files",
out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files",
out=log)
#
if params.value_outside_atoms == 'mean':
print >> log, "\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width and params.density_select:
print >> log, "\nHalf width at half height will be used to id boundaries"
if params.soft_mask and sites_cart_all.size() > 0:
print >> log, "\nSoft mask will be applied to model-based mask"
if params.keep_map_size:
print >> log, "\nEntire map will be kept (not cutting out region)"
if params.restrict_map_size:
print >> log, "\nOutput map will be within input map"
if params.lower_bounds and params.upper_bounds:
print >> log, "Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" % (
tuple(list(params.lower_bounds) + list(params.upper_bounds)))
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure=xray_structure,
map_data=map_data.as_double(),
box_cushion=params.box_cushion,
selection=selection,
density_select=params.density_select,
threshold=params.density_select_threshold,
get_half_height_width=params.get_half_height_width,
mask_atoms=params.mask_atoms,
soft_mask=params.soft_mask,
soft_mask_radius=params.soft_mask_radius,
mask_atoms_atom_radius=params.mask_atoms_atom_radius,
value_outside_atoms=params.value_outside_atoms,
keep_map_size=params.keep_map_size,
restrict_map_size=params.restrict_map_size,
lower_bounds=params.lower_bounds,
upper_bounds=params.upper_bounds,
extract_unique=params.extract_unique,
chain_type=params.chain_type,
sequence=sequence,
solvent_content=params.solvent_content,
molecular_mass=params.molecular_mass,
resolution=params.resolution,
ncs_object=ncs_object,
symmetry=params.symmetry,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy = ph_box
if (inputs and inputs.crystal_symmetry and inputs.ccp4_map
and inputs.crystal_symmetry.unit_cell().parameters()
and inputs.ccp4_map.unit_cell_parameters) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print >> log, "\nNOTE: Mismatch of unit cell parameters from CCP4 map:"
print >>log,"Unit cell from CCP4 map 'unit cell parameters': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.ccp4_map.unit_cell_parameters)
print >>log,"Unit cell from CCP4 map 'map grid': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.crystal_symmetry.unit_cell().parameters())
print >>log,"\nInterpreting this as the 'unit cell parameters' was "+\
"original map \ndimension and 'map grid' is the "+\
"portion actually in the map that was supplied here.\n"
box.unit_cell_parameters_from_ccp4_map = inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map = None
box.unit_cell_parameters_deduced_from_map_grid = None
# ncs_object is original
# box.ncs_object is shifted by shift_cart
print >> log, "Box cell dimensions: (%.2f, %.2f, %.2f) A" % (
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if params.keep_origin:
print >> log, "Box origin is at grid position of : (%d, %d, %d) " % (
tuple(box.origin_shift_grid_units(reverse=True)))
print >> log, "Box origin is at coordinates: (%.2f, %.2f, %.2f) A" % (
tuple(-col(box.shift_cart)))
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
# NOTE: box object is always shifted to place origin at (0,0,0)
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
if (not params.keep_origin):
if box.shift_cart:
print >>log,\
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A" %(
tuple(box.shift_cart))
else:
print >>log,"\nOutput files are in same location as original: origin "+\
"is at (0,0,0)"
else: # keep_origin
print >> log, "\nOutput files are in same location as original, just cut out."
print >> log, "Note that output maps are only valid in the cut out region.\n"
if params.keep_origin:
ph_box_original_location = ph_box.deep_copy()
sites_cart = box.shift_sites_cart_back(
box.xray_structure_box.sites_cart())
xrs_offset = ph_box_original_location.extract_xray_structure(
crystal_symmetry=box.xray_structure_box.crystal_symmetry(
)).replace_sites_cart(new_sites=sites_cart)
ph_box_original_location.adopt_xray_structure(xrs_offset)
box.hierarchy_original_location = ph_box_original_location
else:
box.hierarchy_original_location = None
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues > 0:
if (params.output_file_name_prefix is None):
file_name = "%s_box.pdb" % output_prefix
else:
file_name = "%s.pdb" % params.output_file_name_prefix
if params.keep_origin: # Keeping origin
print >> log, "Writing boxed PDB with box unit cell and in "+\
"original\n position to: %s"%(
file_name)
ph_box_original_location.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
else: # write box PDB in box cell
print >> log, "Writing shifted boxed PDB to file: %s" % file_name
ph_box.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
# Write NCS file if NCS
if ncs_object and ncs_object.max_operators() > 0:
if (params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec" % output_prefix
else:
output_symmetry_file = "%s.ncs_spec" % params.output_file_name_prefix
if params.keep_origin:
if params.symmetry_file:
print >> log, "\nDuplicating symmetry in %s and writing to %s" % (
params.symmetry_file, output_symmetry_file)
else:
print >> log, "\nWriting symmetry to %s" % (
output_symmetry_file)
ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
else:
print >> log, "\nOffsetting symmetry in %s and writing to %s" % (
params.symmetry_file, output_symmetry_file)
box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
# Write ccp4 map. Shift back to original location if keep_origin=True
if ("ccp4" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.ccp4" % output_prefix
else:
file_name = "%s.ccp4" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing boxed map with box unit_cell and "+\
"original\n position to CCP4 formatted file: %s"%file_name
else:
print >> log, "Writing box map shifted to (0,0,0) to CCP4 "+\
"formatted file: %s"%file_name
box.write_ccp4_map(file_name=file_name,
shift_back=params.keep_origin)
# Write xplor map. Shift back if keep_origin=True
if ("xplor" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.xplor" % output_prefix
else:
file_name = "%s.xplor" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing boxed map with box unit_cell and original "+\
"position\n to X-plor formatted file: %s"%file_name
else:
print >> log, "Writing box_map shifted to (0,0,0) to X-plor "+\
"formatted file: %s"%file_name
box.write_xplor_map(file_name=file_name,
shift_back=params.keep_origin)
# Write mtz map coeffs. Shift back if keep_origin=True
if ("mtz" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.mtz" % output_prefix
else:
file_name = "%s.mtz" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing map coefficients with box_map unit_cell"+\
" but position matching\n "+\
" original position to MTZ file: %s"%file_name
else:
print >> log, "Writing box_map coefficients shifted to (0,0,0) "+\
"to MTZ file: %s"%file_name
if (map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(
map_data=box.map_box,
unit_cell=box.xray_structure_box.unit_cell())
box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor,
file_name=file_name,
shift_back=params.keep_origin)
print >> log
return box
def __init__(
self,
fmodels,
model,
params,
target_weights,
macro_cycle,
ncs_manager=None,
log=None):
if log is None:
log = sys.stdout
# self.ncs_manager = ncs_manager
self.nproc = params.main.nproc
if self.nproc is Auto:
self.nproc = 1
self.verbose = params.den.verbose
self.log = log
self.fmodels = fmodels
self.model = model
self.params = params
self.target_weights = target_weights
self.adp_refinement_manager = None
self.macro_cycle = macro_cycle
self.tan_b_iso_max = 0
self.random_seed = params.main.random_seed
den_manager = model.restraints_manager. \
geometry.den_manager
print_statistics.make_header("DEN refinement", out=self.log)
pdb_hierarchy = self.model.pdb_hierarchy(sync_with_xray_structure=True)
if den_manager.get_n_proxies() == 0:
print_statistics.make_sub_header(
"DEN restraint nework", out = self.log)
den_manager.build_den_proxies(pdb_hierarchy=pdb_hierarchy)
den_manager.build_den_restraints()
den_manager.show_den_summary(
sites_cart=self.model.xray_structure.sites_cart())
if den_manager.params.output_kinemage:
den_manager.output_kinemage(
self.model.xray_structure.sites_cart())
print_statistics.make_sub_header(
"coordinate minimization before annealing", out=self.log)
self.minimize(ca_only=self.params.den.minimize_c_alpha_only)
self.save_scatterers_local = fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
#DEN refinement start, turn on
if params.den.optimize:
grid = den_manager.get_optimization_grid()
print >> log, \
"Running DEN torsion optimization on %d processors..." % \
params.main.nproc
else:
grid = [(params.den.gamma, params.den.weight)]
grid_results = []
grid_so = []
if "torsion" in params.den.annealing_type:
print >> self.log, "Running torsion simulated annealing"
if ( (params.den.optimize) and
( (self.nproc is Auto) or (self.nproc > 1) )):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_torsion,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError(("DEN weight optimization failed:"+
"\n%s\nThis is a "+
"serious error; please contact [email protected].") % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_torsion(
grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_torsion(grid_results)
elif "cartesian" in params.den.annealing_type:
print >> self.log, "Running Cartesian simulated annealing"
if ( (params.den.optimize) and
( (self.nproc is Auto) or (self.nproc > 1) )):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_cartesian,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError(("DEN weight optimization failed:"+
"\n%s\nThis is a "+
"serious error; please contact [email protected].") % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_cartesian(
grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_cartesian(grid_results)
else:
raise "error in DEN annealing type"
low_r_free = 1.0
best_xray_structure = None
best_eq_distances = None
best_gamma = None
best_weight = None
best_so_i = None
for i, result in enumerate(grid_results):
cur_r_free = result[2]
if cur_r_free < low_r_free:
low_r_free = cur_r_free
best_gamma = result[0]
best_weight = result[1]
best_xray_structure = result[3]
best_eq_distances = result[4]
best_so_i = i
assert best_xray_structure is not None
if params.den.optimize:
print >> self.log, "\nbest gamma: %.1f" % best_gamma
print >> self.log, "best weight: %.1f\n" % best_weight
if params.den.verbose:
if len(grid_so) >= (best_so_i+1):
print >> self.log, "\nBest annealing results:\n"
print >> self.log, grid_so[best_so_i]
fmodels.fmodel_xray().xray_structure.replace_scatterers(
best_xray_structure.deep_copy())
fmodels.update_xray_structure(
xray_structure = fmodels.fmodel_xray().xray_structure,
update_f_calc = True)
utils.assert_xray_structures_equal(
x1 = fmodels.fmodel_xray().xray_structure,
x2 = model.xray_structure)
model.restraints_manager.geometry.\
den_manager.import_eq_distances(eq_distances=best_eq_distances)
self.model.restraints_manager.geometry.update_dihedral_ncs_restraints(
sites_cart=self.model.xray_structure.sites_cart(),
pdb_hierarchy=self.model.pdb_hierarchy(sync_with_xray_structure=True),
log=self.log)
def run(args,
crystal_symmetry=None,
pdb_hierarchy=None,
map_data=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if (log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message = """\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:""" % h
if (len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args=args,
cmd_cs=crystal_symmetry,
master_params=master_phil)
params = inputs.params.extract()
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names = [params.pdb_file]
if (len(inputs.pdb_file_names) != 1 and not params.density_select
and not pdb_hierarchy):
raise Sorry("PDB file is needed unless density_select is set.")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names) > 0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy = None
# Map or map coefficients
map_coeff = None
if (not map_data):
# read first mtz file
if ((len(inputs.reflection_file_names) > 0)
or (params.map_coefficients_file is not None)):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(
params.map_coefficients_file)
else:
inputs.reflection_file_names[
0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name=inputs.reflection_file_names[0],
label=params.label,
type="complex",
log=log)
fft_map = map_coeff.fft_map(
resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix = os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ((inputs.ccp4_map is not None)
or (params.ccp4_map_file is not None)):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ", out=log)
map_data = ccp4_map.data #map_data()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix = None
# final check that map_data exists
if (map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names) > 0:
output_prefix = os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix = map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy = iotbx.pdb.input(
source_info='', lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string=params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'" % params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(radius=params.selection_radius,
selection=selection)
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files",
out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files",
out=log)
#
if params.value_outside_atoms == 'mean':
print >> log, "\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width:
print >> log, "\nHalf width at half height will be used to id boundaries"
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure=xray_structure,
map_data=map_data.as_double(),
box_cushion=params.box_cushion,
selection=selection,
density_select=params.density_select,
threshold=params.density_select_threshold,
get_half_height_width=params.get_half_height_width,
mask_atoms=params.mask_atoms,
soft_mask=params.soft_mask,
soft_mask_radius=params.soft_mask_radius,
mask_atoms_atom_radius=params.mask_atoms_atom_radius,
value_outside_atoms=params.value_outside_atoms,
)
if box.initial_shift_cart:
print >> log, "\nInitial coordinate shift will be (%.1f,%.1f,%.1f)\n" % (
box.initial_shift_cart)
if box.total_shift_cart:
print >> log, "Final coordinate shift: (%.1f,%.1f,%.1f)" % (
box.total_shift_cart)
print >> log, "Final cell dimensions: (%.1f,%.1f,%.1f)\n" % (
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy = ph_box
if not write_output_files:
return box
if (params.output_file_name_prefix is None):
file_name = "%s_box.pdb" % output_prefix
else:
file_name = "%s.pdb" % params.output_file_name_prefix
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
ph_box.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
if ("ccp4" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.ccp4" % output_prefix
else:
file_name = "%s.ccp4" % params.output_file_name_prefix
print >> log, "writing map to CCP4 formatted file: %s" % file_name
box.write_ccp4_map(file_name=file_name)
if ("xplor" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.xplor" % output_prefix
else:
file_name = "%s.xplor" % params.output_file_name_prefix
print >> log, "writing map to X-plor formatted file: %s" % file_name
box.write_xplor_map(file_name=file_name)
if ("mtz" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.mtz" % output_prefix
else:
file_name = "%s.mtz" % params.output_file_name_prefix
print >> log, "writing map coefficients to MTZ file: %s" % file_name
if (map_coeff is not None): d_min = map_coeff.d_min()
else:
d_min = maptbx.d_min_from_map(
map_data=box.map_box,
unit_cell=box.xray_structure_box.unit_cell())
box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor,
file_name=file_name)
if params.ncs_file:
if (params.output_file_name_prefix is None):
output_ncs_file = "%s_box.ncs_spec" % output_prefix
else:
output_ncs_file = "%s.ncs_spec" % params.output_file_name_prefix
print >> log, "\nOffsetting NCS in %s and writing to %s" % (
params.ncs_file, output_ncs_file)
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
ncs_object.read_ncs(params.ncs_file, log=log)
ncs_object.display_all(log=log)
if not ncs_object or ncs_object.max_operators() < 1:
print >> log, "Skipping...no NCS available"
elif box.total_shift_cart:
from scitbx.math import matrix
print >>log,"Shifting NCS operators "+\
"based on coordinate shift of (%7.1f,%7.1f,%7.1f)" %(
tuple(box.total_shift_cart))
ncs_object = ncs_object.coordinate_offset(
coordinate_offset=matrix.col(box.total_shift_cart))
ncs_object.display_all(log=log)
ncs_object.format_all_for_group_specification(
file_name=output_ncs_file)
box.ncs_object = ncs_object
else:
box.ncs_object = None
print >> log
return box
def run(args, crystal_symmetry=None, log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil)
params = inputs.params.extract()
# PDB file
if params.pdb_file and not inputs.pdb_file_names:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select):
raise Sorry("PDB file is needed unless density_select is set.")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
if(inputs.ccp4_map is None):
if(len(inputs.reflection_file_names)!=1):
raise Sorry("Map or map coefficients file is needed.")
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
else:
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ")
map_data = ccp4_map.map_data()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
#
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'"%params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
box_cushion = params.box_cushion,
selection = selection,
density_select = params.density_select,
threshold = params.density_select_threshold)
if box.initial_shift_cart:
print >>log,"\nInitial coordinate shift will be (%.1f,%.1f,%.1f)\n" %(
box.initial_shift_cart)
if box.total_shift_cart:
print >>log,"Final coordinate shift: (%.1f,%.1f,%.1f)" %(
box.total_shift_cart)
print >>log,"Final cell dimensions: (%.1f,%.1f,%.1f)\n" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
ph_box.write_pdb_file(file_name=file_name, crystal_symmetry =
box.xray_structure_box.crystal_symmetry())
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
print >> log, "writing map to CCP4 formatted file: %s"%file_name
box.write_ccp4_map(file_name=file_name)
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
print >> log, "writing map to X-plor formatted file: %s"%file_name
box.write_xplor_map(file_name=file_name)
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print >> log, "writing map coefficients to MTZ file: %s"%file_name
if(map_coeff is not None): d_min = map_coeff.d_min()
else:
d_min = maptbx.d_min_from_map(map_data=box.map_box,
unit_cell=box.xray_structure_box.unit_cell())
box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor, file_name=file_name)
if params.ncs_file:
if(params.output_file_name_prefix is None):
output_ncs_file = "%s_box.ncs_spec"%output_prefix
else: output_ncs_file = "%s.ncs_spec"%params.output_file_name_prefix
print >>log,"\nOffsetting NCS in %s and writing to %s" %(
params.ncs_file,output_ncs_file)
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
ncs_object.read_ncs(params.ncs_file,log=log)
ncs_object.display_all(log=log)
if not ncs_object or ncs_object.max_operators()<1:
print >>log,"Skipping...no NCS available"
elif box.total_shift_cart:
from scitbx.math import matrix
print >>log,"Shifting NCS operators "+\
"based on coordinate shift of (%7.1f,%7.1f,%7.1f)" %(
tuple(box.total_shift_cart))
ncs_object=ncs_object.coordinate_offset(
coordinate_offset=matrix.col(box.total_shift_cart))
ncs_object.display_all(log=log)
ncs_object.format_all_for_group_specification(
file_name=output_ncs_file)
box.ncs_object=ncs_object
else:
box.ncs_object=None
print >> log
return box
def run(args, crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
mask_data=None,
half_map_data_list=None,
half_map_labels_list=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0 and not pdb_hierarchy):
print(default_message)
master_phil.show(prefix=" ")
return
# Process inputs ignoring symmetry conflicts just to get the value of
# ignore_symmetry_conflicts...
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil,
suppress_symmetry_related_errors=True)
params = inputs.params.extract()
# Now process inputs for real and write a nice error message if necessary.
try:
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil,
suppress_symmetry_related_errors=params.ignore_symmetry_conflicts)
except Exception as e:
if str(e).find("symmetry mismatch ")>1:
raise Sorry(str(e)+"\nTry 'ignore_symmetry_conflicts=True'")
else:
raise e
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds=lower_bounds
if upper_bounds:
params.upper_bounds=upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select and not
params.mask_select and not
pdb_hierarchy and not params.keep_map_size and not params.upper_bounds
and not params.extract_unique and not params.bounds_match_this_file):
raise Sorry("PDB file is needed unless extract_unique, "+
"density_select, mask_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms )):
raise Sorry("PDB file is needed for mask_atoms")
if params.soft_mask and (not params.resolution) and \
(len(inputs.pdb_file_names)!=1 and not pdb_hierarchy):
raise Sorry("Need resolution for soft_mask without PDB file")
if ((params.density_select or params.mask_select) and params.keep_map_size):
raise Sorry("Cannot set both density_select/mask_select and keep_map_size")
if ((params.density_select or params.mask_select) and params.upper_bounds):
raise Sorry("Cannot set both density_select/mask_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique):
if (not params.resolution):
raise Sorry("Please set resolution for extract_unique")
if (not params.symmetry) and (not params.symmetry_file) and \
(not ncs_object):
raise Sorry(
"Please supply a symmetry file or symmetry for extract_unique (you "+
"\ncan try symmetry=ALL if you do not know your symmetry or "+
"symmetry=C1 if \nthere is none)")
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
ncs_object.set_unit_ncs()
if params.keep_input_unit_cell_and_grid and (
(params.output_unit_cell_grid is not None ) or
(params.output_unit_cell is not None ) ):
raise Sorry("If you set keep_input_unit_cell_and_grid then you cannot "+\
"set \noutput_unit_cell_grid or output_unit_cell")
if (write_output_files) and ("mtz" in params.output_format) and (
(params.keep_origin) and (not params.keep_map_size)):
print("\nNOTE: Skipping write of mtz file as keep_origin=True and \n"+\
"keep_map_size is False\n")
params.output_format=remove_element(params.output_format,element='mtz')
if (write_output_files) and ("mtz" in params.output_format) and (
(params.extract_unique)):
print("\nNOTE: Skipping write of mtz file as extract_unique=True\n")
params.output_format=remove_element(params.output_format,element='mtz')
if params.output_origin_match_this_file or params.bounds_match_this_file:
if params.output_origin_match_this_file:
fn=params.output_origin_match_this_file
if params.bounds_match_this_file:
raise Sorry("Cannot match origin and bounds at same time")
else:
fn=params.bounds_match_this_file
if not params.ccp4_map_file:
raise Sorry(
"Need to specify your input file with ccp4_map_file=xxx if you use "+
"output_origin_match_this_file=xxxx or bounds_match_this_file=xxxx")
af = any_file(fn)
if (af.file_type == 'ccp4_map'):
origin=af.file_content.data.origin()
if params.output_origin_match_this_file:
params.output_origin_grid_units=origin
print("Origin of (%s,%s,%s) taken from %s" %(
origin[0],origin[1],origin[2],fn))
else:
all=af.file_content.data.all()
params.lower_bounds=origin
print("Lower bounds of (%s,%s,%s) taken from %s" %(
params.lower_bounds[0],params.lower_bounds[1],
params.lower_bounds[2],fn))
params.upper_bounds=list(col(origin)+col(all)-col((1,1,1)))
print("upper bounds of (%s,%s,%s) taken from %s" %(
params.upper_bounds[0],params.upper_bounds[1],
params.upper_bounds[2],fn))
params.bounds_are_absolute=True
else:
raise Sorry("Unable to interpret %s as map file" %(fn))
if params.output_origin_grid_units is not None and params.keep_origin:
params.keep_origin=False
print("Setting keep_origin=False as output_origin_grid_units is set")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
input_unit_cell_grid=None
input_unit_cell=None
input_map_labels=None
if (not map_data):
# read first mtz file
if ( (len(inputs.reflection_file_names) > 0) or
(params.map_coefficients_file is not None) ):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(params.map_coefficients_file)
else:
inputs.reflection_file_names[0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
if not crystal_symmetry: crystal_symmetry=map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ( (inputs.ccp4_map is not None) or
(params.ccp4_map_file is not None) ):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ",out=log)
if not crystal_symmetry: crystal_symmetry=ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
input_unit_cell_grid=ccp4_map.unit_cell_grid
input_unit_cell=ccp4_map.unit_cell_parameters
input_map_labels=ccp4_map.get_labels()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix=None
if params.half_map_list and (not half_map_data_list):
if not params.extract_unique:
raise Sorry("Can only use half_map_with extract_unique")
print ("Reading half-maps",params.half_map_list)
half_map_data_list=[]
half_map_labels_list=[]
for fn in params.half_map_list:
print("Reading half map from %s" %(fn),file=log)
af = any_file(fn)
print_statistics.make_sub_header("CCP4 map", out=log)
h_ccp4_map = af.file_content
h_ccp4_map.show_summary(prefix=" ",out=log)
h_map_data = h_ccp4_map.data
half_map_data_list.append(h_map_data)
half_map_labels_list.append(h_ccp4_map.get_labels())
if params.map_scale_factor:
print("Applying scale factor of %s to map data on read-in" %(
params.map_scale_factor))
map_data=map_data*params.map_scale_factor
if params.output_origin_grid_units is not None:
origin_to_match=tuple(params.output_origin_grid_units)
else:
origin_to_match=None
if origin_to_match:
sc=[]
for x,o,a in zip(crystal_symmetry.unit_cell().parameters()[:3],
origin_to_match,
map_data.all()):
sc.append(-x*o/a)
shift_cart_for_origin_to_match=tuple(sc)
else:
origin_to_match=None
shift_cart_for_origin_to_match=None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry=crystal_symmetry
# final check that map_data exists
if(map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
if not params.selection: params.selection="all"
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print("Selection string: selection='%s'"%params.selection, file=log)
print(" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size()), file=log)
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file,log=log)
print("Total of %s operators read" %(ncs_object.max_operators()), file=log)
if not ncs_object or ncs_object.max_operators()<1:
print("No symmetry available", file=log)
if ncs_object:
n_ops=max(1,ncs_object.max_operators())
else:
n_ops=1
# Get sequence if extract_unique is set
sequence=None
if params.extract_unique or params.mask_select:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence
remove_duplicates=True
else:
remove_duplicates=False
from iotbx.bioinformatics import get_sequences
sequence=(" ".join(get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if params.chain_type in ['None',None]: params.chain_type=None
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None,'PROTEIN']:
n_protein=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='PROTEIN'))
else:
n_protein=0
if params.chain_type in [None,'RNA']:
n_rna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='RNA'))
else:
n_rna=0
if params.chain_type in [None,'DNA']:
n_dna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='DNA'))
else:
n_dna=0
params.molecular_mass=n_ops*(n_protein*110+(n_rna+n_dna)*330)
print("\nEstimate of molecular mass is %.0f " %(params.molecular_mass), file=log)
if params.density_select or params.mask_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
if params.value_outside_atoms=='mean':
print("\nValue outside atoms mask will be set to mean inside mask", file=log)
if params.get_half_height_width and params.density_select:
print("\nHalf width at half height will be used to id boundaries", file=log)
if params.soft_mask and sites_cart_all.size()>0:
print("\nSoft mask will be applied to model-based mask", file=log)
elif params.soft_mask:
print ("\nSoft mask will be applied to outside of map box",file=log)
if params.keep_map_size:
print("\nEntire map will be kept (not cutting out region)", file=log)
if params.restrict_map_size:
print("\nOutput map will be within input map", file=log)
if params.lower_bounds and params.upper_bounds:
print("Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" %(
tuple(list(params.lower_bounds)+list(params.upper_bounds))), file=log)
if mask_data:
mask_data=mask_data.as_double()
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
mask_data = mask_data,
box_cushion = params.box_cushion,
selection = selection,
mask_select = params.mask_select,
density_select = params.density_select,
threshold = params.density_select_threshold,
get_half_height_width = params.get_half_height_width,
mask_atoms = params.mask_atoms,
soft_mask = params.soft_mask,
soft_mask_radius = params.soft_mask_radius,
mask_atoms_atom_radius = params.mask_atoms_atom_radius,
value_outside_atoms = params.value_outside_atoms,
keep_map_size = params.keep_map_size,
restrict_map_size = params.restrict_map_size,
lower_bounds = params.lower_bounds,
upper_bounds = params.upper_bounds,
bounds_are_absolute = params.bounds_are_absolute,
zero_outside_original_map = params.zero_outside_original_map,
extract_unique = params.extract_unique,
target_ncs_au_file = params.target_ncs_au_file,
regions_to_keep = params.regions_to_keep,
box_buffer = params.box_buffer,
soft_mask_extract_unique = params.soft_mask_extract_unique,
mask_expand_ratio = params.mask_expand_ratio,
keep_low_density = params.keep_low_density,
chain_type = params.chain_type,
sequence = sequence,
solvent_content = params.solvent_content,
molecular_mass = params.molecular_mass,
resolution = params.resolution,
ncs_object = ncs_object,
symmetry = params.symmetry,
half_map_data_list = half_map_data_list,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy=ph_box
if params.mask_select:
print("\nSolvent content used in mask_select: %.3f " %(
box.get_solvent_content()),file=log)
if (inputs and
inputs.crystal_symmetry and inputs.ccp4_map and
inputs.crystal_symmetry.unit_cell().parameters() and
inputs.ccp4_map.unit_cell_parameters ) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print("\nNOTE: Input CCP4 map is only part of unit cell:", file=log)
print("Full unit cell ('unit cell parameters'): "+\
"(%.1f, %.1f, %.1f, %.1f, %.1f, %.1f) A" %tuple(
inputs.ccp4_map.unit_cell_parameters), file=log)
print("Size of CCP4 map 'map unit cell': "+\
"(%.1f, %.1f, %.1f, %.1f, %.1f, %.1f) A" %tuple(
inputs.crystal_symmetry.unit_cell().parameters()), file=log)
print("Full unit cell as grid units: (%s, %s, %s)" %(
inputs.ccp4_map.unit_cell_grid), file=log)
print("Map unit cell as grid units: (%s, %s, %s)" %(
map_data.all()), file=log)
box.unit_cell_parameters_from_ccp4_map=inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map=None
box.unit_cell_parameters_deduced_from_map_grid=None
if box.pdb_outside_box_msg:
print(box.pdb_outside_box_msg, file=log)
# NOTE: box object is always shifted to place origin at (0,0,0)
# NOTE ON ORIGIN SHIFTS: The shifts are applied locally here. The box
# object is not affected and always has the origin at (0,0,0)
# output_box is copy of box with shift_cart corresponding to the output
# files. Normally this is the same as the original shift_cart. However
# if user has specified a new output origin it will differ.
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
# output_origin_grid_units=10,10,10: output origin is at (10,10,10)
# ncs_object is original
# box.ncs_object is shifted by shift_cart
# output_box.ncs_object is shifted back by -new shift_cart
# Additional note on output unit_cell and grid_units.
# The ccp4-style output map can specify the unit cell and grid units
# corresponding to that cell. This can be separate from the origin and
# number of grid points in the map as written. If specified, write these
# out to the output ccp4 map and also use this unit cell for writing
# any output PDB files
from copy import deepcopy
output_box=deepcopy(box) # won't use box below here except to return it
print("\nBox cell dimensions: (%.2f, %.2f, %.2f) A" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3]), file=log)
if box.shift_cart:
print("Working origin moved from grid position of"+\
": (%d, %d, %d) to (0,0,0) " %(
tuple(box.origin_shift_grid_units(reverse=True))), file=log)
print("Working origin moved from coordinates of:"+\
" (%.2f, %.2f, %.2f) A to (0,0,0)\n" %(
tuple(-col(box.shift_cart))), file=log)
if (params.keep_origin):
print("\nRestoring original position for output files", file=log)
print("Origin will be at grid position of"+\
": (%d, %d, %d) " %(
tuple(box.origin_shift_grid_units(reverse=True))), file=log)
print("\nOutput files will be in same location as original", end=' ', file=log)
if not params.keep_map_size:
print("just cut out.", file=log)
else:
print("keeping entire map", file=log)
print("Note that output maps are only valid in the cut out region.\n", file=log)
else:
if origin_to_match:
output_box.shift_cart=shift_cart_for_origin_to_match
if params.output_origin_grid_units:
print("Output map origin to be shifted to match target", file=log)
print("Placing origin at grid point (%s, %s, %s)" %(
origin_to_match)+"\n"+ \
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart))), file=log)
elif box.shift_cart:
output_box.shift_cart=(0,0,0) # not shifting back
print("Final origin will be at (0,0,0)", file=log)
print("Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart))), file=log)
else:
print("\nOutput files are in same location as original and origin "+\
"is at (0,0,0)\n", file=log)
print("\nBox grid: (%s, %s, %s) " %(output_box.map_box.all()),file=log)
ph_output_box_output_location = ph_box.deep_copy()
if output_box.shift_cart: # shift coordinates and NCS back by shift_cart
# NOTE output_box.shift_cart could be different than box.shift_cart if
# there is a target position for the origin and it is not the same as the
# original origin.
sites_cart = output_box.shift_sites_cart_back(
output_box.xray_structure_box.sites_cart())
xrs_offset = ph_output_box_output_location.extract_xray_structure(
crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
).replace_sites_cart(new_sites = sites_cart)
ph_output_box_output_location.adopt_xray_structure(xrs_offset)
if output_box.ncs_object:
output_box.ncs_object=output_box.ncs_object.coordinate_offset(
tuple(-col(output_box.shift_cart)))
shift_back=True
else:
shift_back=False
if params.keep_input_unit_cell_and_grid and \
(input_unit_cell_grid is not None) and \
(input_unit_cell is not None):
params.output_unit_cell=input_unit_cell
params.output_unit_cell_grid=input_unit_cell_grid
print("Setting output unit cell parameters and unit cell grid to"+\
" match\ninput map file", file=log)
if params.output_unit_cell: # Set output unit cell parameters
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=params.output_unit_cell, space_group="P1")
output_unit_cell=output_crystal_symmetry.unit_cell()
print("Output unit cell set to: %.2f, %.2f, %.2f, %.2f, %.2f, %.2f)" %tuple(
output_crystal_symmetry.unit_cell().parameters()), file=log)
else:
output_crystal_symmetry=None
# ============= Check/set output unit cell grid and cell parameters =======
if params.output_unit_cell_grid or output_crystal_symmetry:
if params.output_unit_cell_grid:
output_unit_cell_grid=params.output_unit_cell_grid
else:
output_unit_cell_grid=output_box.map_box.all()
print("Output unit cell grid set to: (%s, %s, %s)" %tuple(
output_unit_cell_grid), file=log)
expected_output_abc=[]
box_spacing=[]
output_spacing=[]
box_abc=output_box.xray_structure_box.\
crystal_symmetry().unit_cell().parameters()[:3]
if output_crystal_symmetry:
output_abc=output_crystal_symmetry.unit_cell().parameters()[:3]
else:
output_abc=[None,None,None]
for a_box,a_output,n_box,n_output in zip(
box_abc,
output_abc,
output_box.map_box.all(),
output_unit_cell_grid):
expected_output_abc.append(a_box*n_output/n_box)
box_spacing.append(a_box/n_box)
if output_crystal_symmetry:
output_spacing.append(a_output/n_output)
else:
output_spacing.append(a_box/n_box)
if output_crystal_symmetry: # make sure it is compatible...
r0=expected_output_abc[0]/output_abc[0]
r1=expected_output_abc[1]/output_abc[1]
r2=expected_output_abc[2]/output_abc[2]
from libtbx.test_utils import approx_equal
if not approx_equal(r0,r1,eps=0.001) or not approx_equal(r0,r2,eps=0.001):
print("WARNING: output_unit_cell and cell_grid will "+\
"change ratio of grid spacing.\nOld spacings: "+\
"(%.2f, %.2f, %.2f) A " %(tuple(box_spacing))+\
"\nNew spacings: (%.2f, %.2f, %.2f) A \n" %(tuple(output_spacing)), file=log)
else:
output_abc=expected_output_abc
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=list(output_abc)+[90,90,90], space_group="P1")
print("Output unit cell will be: (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f)\n"%(
tuple(output_crystal_symmetry.unit_cell().parameters())), file=log)
else:
output_unit_cell_grid = output_box.map_box.all()
output_crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
# ========== Done check/set output unit cell grid and cell parameters =====
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues>0:
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_output_box_output_location.write_pdb_file(file_name=file_name,
crystal_symmetry = output_crystal_symmetry)
print("Writing boxed PDB with box unit cell to %s" %(
file_name), file=log)
# Write NCS file if NCS
if output_box.ncs_object and output_box.ncs_object.max_operators()>0:
if(params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec"%output_prefix
else:
output_symmetry_file = "%s.ncs_spec"%params.output_file_name_prefix
output_box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
print("\nWriting symmetry to %s" %( output_symmetry_file), file=log)
# Write ccp4 map.
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
from iotbx.mrcfile import create_output_labels
if params.extract_unique:
program_name='map_box using extract_unique'
limitations=["extract_unique"]
else:
program_name='map_box'
limitations=[]
labels=create_output_labels(program_name=program_name,
input_file_name=inputs.ccp4_map_file_name,
input_labels=input_map_labels,
limitations=limitations,
output_labels=params.output_map_labels)
output_box.write_ccp4_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_mean=params.output_ccp4_map_mean,
output_sd=params.output_ccp4_map_sd,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,
output_map_labels=labels,
output_external_origin=params.output_external_origin)
print("Writing boxed map "+\
"to CCP4 formatted file: %s"%file_name, file=log)
if not params.half_map_list:
params.half_map_list=[]
if not output_box.map_box_half_map_list:
output_box.map_box_half_map_list=[]
if not half_map_labels_list:
half_map_labels_list=len(output_box.map_box_half_map_list)*[None]
for hm,labels,fn in zip(
output_box.map_box_half_map_list,
half_map_labels_list,
params.half_map_list): # half maps matching
labels=create_output_labels(program_name=program_name,
input_file_name=fn,
input_labels=labels,
limitations=limitations,
output_labels=params.output_map_labels)
hm_fn="%s_box.ccp4" %( ".".join(os.path.basename(fn).split(".")[:-1]))
output_box.write_ccp4_map(file_name=hm_fn,
map_data=hm,
output_crystal_symmetry=output_crystal_symmetry,
output_mean=params.output_ccp4_map_mean,
output_sd=params.output_ccp4_map_sd,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,
output_map_labels=labels,
output_external_origin=params.output_external_origin)
print ("Writing boxed half map to: %s " %(hm_fn),file=log)
# Write xplor map. Shift back if keep_origin=True
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
output_box.write_xplor_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,)
print("Writing boxed map "+\
"to X-plor formatted file: %s"%file_name, file=log)
# Write mtz map coeffs. Shift back if keep_origin=True
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print("Writing map coefficients "+\
"to MTZ file: %s"%file_name, file=log)
if(map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(map_data=output_box.map_box,
unit_cell=output_box.xray_structure_box.unit_cell())
output_box.map_coefficients(d_min=d_min,
scale_max=params.scale_max,
resolution_factor=params.resolution_factor, file_name=file_name,
shift_back=shift_back)
print(file=log)
return box
def find_tls (params,
pdb_inp,
pdb_hierarchy,
xray_structure,
return_as_list=False,
ignore_pdb_header_groups=False,
out=None) :
if (out is None) :
out = sys.stdout
print_statistics.make_header("Analyzing inputs", out=out)
if (params.random_seed is None) :
params.random_seed = flex.get_random_seed()
random.seed(params.random_seed)
flex.set_random_seed(params.random_seed)
xray_structure.convert_to_isotropic()
sites_cart = xray_structure.sites_cart()
u_cart = None
u_iso = xray_structure.extract_u_iso_or_u_equiv()#*adptbx.u_as_b(1.) # ?
bad_i_seqs = check_adp(u_iso=u_iso, out=out)
if (bad_i_seqs is not None) :
atoms = pdb_hierarchy.atoms()
bad_atom_strings = []
for i_seq in bad_i_seqs[:10] :
atom_str = atoms[i_seq].format_atom_record()
bad_atom_strings.append(atom_str)
if (len(bad_i_seqs) > 10) :
bad_atom_strings.append("... (remaining %d not shown)" %
(len(bad_i_seqs)-10))
raise Sorry(("%d atoms in the model contain isotropic B-factors <= 0:\n"+
"\n".join(bad_atom_strings)) % (len(bad_i_seqs)))
#
ssm = mmtbx.secondary_structure.manager(
pdb_hierarchy = pdb_hierarchy,
sec_str_from_pdb_file = None,
params = None)
alpha_h_selection = ssm.alpha_selection()
secondary_structure_selection = ssm.alpha_selection() | \
ssm.beta_selection() | ssm.base_pair_selection()
if(u_cart is not None):
assert secondary_structure_selection.size() == u_cart.size()
else:
assert secondary_structure_selection.size() == u_iso.size()
ssm.show_summary(log=out)
chains_and_residue_selections, secondary_structure_selection = chains_and_atoms(
pdb_hierarchy = pdb_hierarchy,
secondary_structure_selection = secondary_structure_selection,
out = out)
chains_and_permutations = []
chains_and_atom_selection_strings = []
print_statistics.make_header("Processing chains", out=out)
if (params.nproc is None) :
params.nproc = 1
for crs in chains_and_residue_selections:
print_statistics.make_sub_header("Processing chain '%s'"%crs[0],
out=out)
chain_selection = chain_selection_from_residues(crs[1])
groups, perms = get_model_partitioning(residues = crs[1],
secondary_structure_selection = secondary_structure_selection,
out = out)
#
#print
#selection_arrays = sels_as_selection_arrays(sels = groups)
#merge_groups_by_connectivity(
# pdb_hierarchy = pdb_hierarchy,
# xray_structure = xray_structure,
# selection_arrays = selection_arrays)
#assert 0
#
if(len(perms)==1):
print >> out, " Whole chain is considered as one TLS group."
chains_and_atom_selection_strings.append([crs[0],
permutations_as_atom_selection_string(groups, perms[0])])
else:
print >> out, " Fitting TLS matrices..."
dic = {}
target_best = 1.e+9
if (params.nproc is Auto) or (params.nproc > 1) :
process_perms = analyze_permutations(
groups=groups,
sites_cart=sites_cart,
u_cart=u_cart,
u_iso=u_iso)
from libtbx import easy_mp
stdout_and_targets = easy_mp.pool_map(
processes=params.nproc,
fixed_func=process_perms,
args=perms,
chunksize=100,
func_wrapper="buffer_stdout_stderr")
targets = [ t for so, t in stdout_and_targets ]
for (perm, target) in zip(perms, targets) :
dic.setdefault(len(perm), []).append([target,perm])
else :
for i_perm, perm in enumerate(perms):
if i_perm%500==0:
print >> out, " ...perm %d of %d"%(i_perm, len(perms))
selections = tls_group_selections(groups, perm)
target = 0
for selection in selections:
mo = tls_refinery(
u_cart = u_cart,
u_iso = u_iso,
sites_cart = sites_cart,
selection = selection)
target += mo.f
dic.setdefault(len(perm), []).append([target,perm])
#print " perm %d of %d: target=%8.3f (TLS groups: %s), permutation:"%(
# i_perm, len(perms),target,len(perm)),perm
print >> out, " Best fits:"
print >> out, " No. of Targets"
print >> out, " groups best rand.pick diff. score permutation"
score_best = -1.e+9
perm_choice = None
for k, v in zip(dic.keys(),dic.values()):
t_best = v[0][0]
perm_best = v[0][1]
for v_ in v:
if(v_[0]<t_best):
t_best = v_[0]
perm_best = v_[1]
if(u_cart is not None):
u_cart_ = u_cart.select(chain_selection)
else: u_cart_ = None
if(u_iso is not None):
u_iso_ = u_iso.select(chain_selection)
else: u_iso_ = None
r = tls_refinery_random_groups(
u_cart = u_cart_,
u_iso = u_iso_,
sites_cart = sites_cart.select(chain_selection),
n_groups = k)
score = (r-t_best)/(r+t_best)*100.
print >> out, " %3d %6.3f %6.3f %6.2f %6.3f"%(
k,t_best, r, r-t_best, score), perm_best
if(score > score_best):
score_best = score
perm_choice = perm_best[:]
#
chains_and_permutations.append([crs[0],perm_choice])
chains_and_atom_selection_strings.append([crs[0],
permutations_as_atom_selection_string(groups, perm_choice)])
#
if (pdb_inp is not None) and (not ignore_pdb_header_groups) :
external_tls_selections = external_tls(
pdb_inp = pdb_inp,
pdb_hierarchy = pdb_hierarchy,
sites_cart = sites_cart,
u_iso = u_iso,
out = out)
print_statistics.make_header("SUMMARY", out=out)
#print "Optimal TLS groups:"
#for chain_and_permutation in chains_and_permutations:
# print chain_and_permutation
#print
print >> out, "TLS atom selections for phenix.refine:"
groups_out = cStringIO.StringIO()
selection_strings = []
print >> groups_out, "refinement.refine.adp {"
for r in chains_and_atom_selection_strings:
prefix = "chain '%s'"%r[0]
if(len(r[1])>0 and len(r[1:])>0):
prefix += " and "
for r_ in r[1:]:
for r__ in r_:
if(len(r__)>0):
group_selection = prefix+"(%s)"%r__
print >> groups_out, " tls = \"%s\"" % group_selection
selection_strings.append("%s" % group_selection)
else:
print >> groups_out, " tls = \"%s\"" % prefix
selection_strings.append("%s" % prefix)
print >> groups_out, "}"
print >> out, groups_out.getvalue()
print >> out
#XXX
if 0:
merge_groups_by_connectivity(
pdb_hierarchy = pdb_hierarchy,
xray_structure = xray_structure,
selection_strings = selection_strings)
#XXX
if(len(selection_strings)>0):
total_target = total_score(
pdb_hierarchy = pdb_hierarchy,
sites_cart = sites_cart,
u_iso = u_iso,
selection_strings = selection_strings)
print >> out, "Overall best total target for automatically found groups: %10.1f"%total_target
print >> out
if (return_as_list) :
return selection_strings
else :
return groups_out.getvalue()
def run(args, crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil)
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds=lower_bounds
if upper_bounds:
params.upper_bounds=upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select and not
pdb_hierarchy and not params.keep_map_size and not params.upper_bounds
and not params.extract_unique):
raise Sorry("PDB file is needed unless extract_unique, "+
"density_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms or params.soft_mask )):
raise Sorry("PDB file is needed for mask_atoms or soft_mask")
if (params.density_select and params.keep_map_size):
raise Sorry("Cannot set both density_select and keep_map_size")
if (params.density_select and params.upper_bounds):
raise Sorry("Cannot set both density_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique and not params.resolution):
raise Sorry("Please set resolution for extract_unique")
if (write_output_files) and ("mtz" in params.output_format) and (
(params.keep_origin) and (not params.keep_map_size)):
raise Sorry("Please set output_format=ccp4 to skip mtz or set "+\
"keep_origin=False or keep_map_size=True")
if params.keep_input_unit_cell_and_grid and (
(params.output_unit_cell_grid is not None ) or
(params.output_unit_cell is not None ) ):
raise Sorry("If you set keep_input_unit_cell_and_grid then you cannot "+\
"set \noutput_unit_cell_grid or output_unit_cell")
if params.output_origin_grid_units is not None and params.keep_origin:
params.keep_origin=False
print "Setting keep_origin=False as output_origin_grid_units is set"
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
input_unit_cell_grid=None
input_unit_cell=None
if (not map_data):
# read first mtz file
if ( (len(inputs.reflection_file_names) > 0) or
(params.map_coefficients_file is not None) ):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(params.map_coefficients_file)
else:
inputs.reflection_file_names[0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
if not crystal_symmetry: crystal_symmetry=map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ( (inputs.ccp4_map is not None) or
(params.ccp4_map_file is not None) ):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ",out=log)
if not crystal_symmetry: crystal_symmetry=ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
input_unit_cell_grid=ccp4_map.unit_cell_grid
input_unit_cell=ccp4_map.unit_cell_parameters
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix=None
if params.output_origin_grid_units is not None:
origin_to_match=tuple(params.output_origin_grid_units)
else:
origin_to_match=None
if origin_to_match:
sc=[]
for x,o,a in zip(crystal_symmetry.unit_cell().parameters()[:3],
origin_to_match,
map_data.all()):
sc.append(-x*o/a)
shift_cart_for_origin_to_match=tuple(sc)
else:
origin_to_match=None
shift_cart_for_origin_to_match=None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry=crystal_symmetry
# final check that map_data exists
if(map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'"%params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file,log=log)
print >>log,"Total of %s operators read" %(ncs_object.max_operators())
if not ncs_object or ncs_object.max_operators()<1:
print >>log,"No symmetry available"
if ncs_object:
n_ops=max(1,ncs_object.max_operators())
else:
n_ops=1
# Get sequence if extract_unique is set
sequence=None
if params.extract_unique:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence and multiply
remove_duplicates=True
else:
remove_duplicates=False
from iotbx.bioinformatics import get_sequences
sequence=n_ops * (" ".join(get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None,'PROTEIN']:
n_protein=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='PROTEIN'))
else:
n_protein=0
if params.chain_type in [None,'RNA']:
n_rna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='RNA'))
else:
n_rna=0
if params.chain_type in [None,'DNA']:
n_dna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='DNA'))
else:
n_dna=0
params.molecular_mass=n_protein*110+(n_rna+n_dna)*330
elif not params.molecular_mass:
raise Sorry("Need a sequence file or molecular mass for extract_unique")
else:
molecular_mass=None
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
if params.value_outside_atoms=='mean':
print >>log,"\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width and params.density_select:
print >>log,"\nHalf width at half height will be used to id boundaries"
if params.soft_mask and sites_cart_all.size()>0:
print >>log,"\nSoft mask will be applied to model-based mask"
if params.keep_map_size:
print >>log,"\nEntire map will be kept (not cutting out region)"
if params.restrict_map_size:
print >>log,"\nOutput map will be within input map"
if params.lower_bounds and params.upper_bounds:
print >>log,"Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" %(
tuple(list(params.lower_bounds)+list(params.upper_bounds)))
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
box_cushion = params.box_cushion,
selection = selection,
density_select = params.density_select,
threshold = params.density_select_threshold,
get_half_height_width = params.get_half_height_width,
mask_atoms = params.mask_atoms,
soft_mask = params.soft_mask,
soft_mask_radius = params.soft_mask_radius,
mask_atoms_atom_radius = params.mask_atoms_atom_radius,
value_outside_atoms = params.value_outside_atoms,
keep_map_size = params.keep_map_size,
restrict_map_size = params.restrict_map_size,
lower_bounds = params.lower_bounds,
upper_bounds = params.upper_bounds,
extract_unique = params.extract_unique,
chain_type = params.chain_type,
sequence = sequence,
solvent_content = params.solvent_content,
molecular_mass = params.molecular_mass,
resolution = params.resolution,
ncs_object = ncs_object,
symmetry = params.symmetry,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy=ph_box
if (inputs and # XXX fix or remove this
inputs.crystal_symmetry and inputs.ccp4_map and
inputs.crystal_symmetry.unit_cell().parameters() and
inputs.ccp4_map.unit_cell_parameters ) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print >>log,"\nNOTE: Mismatch of unit cell parameters from CCP4 map:"
print >>log,"Unit cell from CCP4 map 'unit cell parameters': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.ccp4_map.unit_cell_parameters)
print >>log,"Unit cell from CCP4 map 'map grid': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.crystal_symmetry.unit_cell().parameters())
print >>log,"\nInterpreting this as the 'unit cell parameters' was "+\
"original map \ndimension and 'map grid' is the "+\
"portion actually in the map that was supplied here.\n"
box.unit_cell_parameters_from_ccp4_map=inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map=None
box.unit_cell_parameters_deduced_from_map_grid=None
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
# NOTE: box object is always shifted to place origin at (0,0,0)
# NOTE ON ORIGIN SHIFTS: The shifts are applied locally here. The box
# object is not affected and always has the origin at (0,0,0)
# output_box is copy of box with shift_cart corresponding to the output
# files. Normally this is the same as the original shift_cart. However
# if user has specified a new output origin it will differ.
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
# output_origin_grid_units=10,10,10: output origin is at (10,10,10)
# ncs_object is original
# box.ncs_object is shifted by shift_cart
# output_box.ncs_object is shifted back by -new shift_cart
# Additional note on output unit_cell and grid_units.
# The ccp4-style output map can specify the unit cell and grid units
# corresponding to that cell. This can be separate from the origin and
# number of grid points in the map as written. If specified, write these
# out to the output ccp4 map and also use this unit cell for writing
# any output PDB files
from copy import deepcopy
output_box=deepcopy(box) # won't use box below here except to return it
print >>log,"\nBox cell dimensions: (%.2f, %.2f, %.2f) A" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if box.shift_cart:
print>>log,"Working origin moved from grid position of"+\
": (%d, %d, %d) to (0,0,0) " %(
tuple(box.origin_shift_grid_units(reverse=True)))
print>>log,"Working origin moved from coordinates of:"+\
" (%.2f, %.2f, %.2f) A to (0,0,0)\n" %(
tuple(-col(box.shift_cart)))
if (params.keep_origin):
print >>log,"\nRestoring original position for output files"
print >>log,"Origin will be at grid position of"+\
": (%d, %d, %d) " %(
tuple(box.origin_shift_grid_units(reverse=True)))
print >>log,\
"\nOutput files will be in same location as original",
if not params.keep_map_size:
print >>log,"just cut out."
else:
print >>log,"keeping entire map"
print >>log,"Note that output maps are only valid in the cut out region.\n"
else:
if origin_to_match:
output_box.shift_cart=shift_cart_for_origin_to_match
if params.output_origin_grid_units:
print >>log,"Output map origin to be shifted to match target"
print >>log, "Placing origin at grid point (%s, %s, %s)" %(
origin_to_match)+"\n"+ \
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart)))
elif box.shift_cart:
output_box.shift_cart=(0,0,0) # not shifting back
print >>log,"Final origin will be at (0,0,0)"
print >>log,\
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart)))
else:
print >>log,\
"\nOutput files are in same location as original and origin "+\
"is at (0,0,0)\n"
ph_output_box_output_location = ph_box.deep_copy()
if output_box.shift_cart: # shift coordinates and NCS back by shift_cart
# NOTE output_box.shift_cart could be different than box.shift_cart if
# there is a target position for the origin and it is not the same as the
# original origin.
sites_cart = output_box.shift_sites_cart_back(
output_box.xray_structure_box.sites_cart())
xrs_offset = ph_output_box_output_location.extract_xray_structure(
crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
).replace_sites_cart(new_sites = sites_cart)
ph_output_box_output_location.adopt_xray_structure(xrs_offset)
if output_box.ncs_object:
output_box.ncs_object=output_box.ncs_object.coordinate_offset(
tuple(-col(output_box.shift_cart)))
shift_back=True
else:
shift_back=False
if params.keep_input_unit_cell_and_grid and \
(input_unit_cell_grid is not None) and \
(input_unit_cell is not None):
params.output_unit_cell=input_unit_cell
params.output_unit_cell_grid=input_unit_cell_grid
print >>log,"Setting output unit cell parameters and unit cell grid to"+\
" match\ninput map file"
if params.output_unit_cell: # Set output unit cell parameters
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=params.output_unit_cell, space_group="P1")
output_unit_cell=output_crystal_symmetry.unit_cell()
print >>log,\
"Output unit cell set to: %.2f, %.2f, %.2f, %.2f, %.2f, %.2f)" %tuple(
output_crystal_symmetry.unit_cell().parameters())
else:
output_crystal_symmetry=None
# ============= Check/set output unit cell grid and cell parameters =======
if params.output_unit_cell_grid or output_crystal_symmetry:
if params.output_unit_cell_grid:
output_unit_cell_grid=params.output_unit_cell_grid
else:
output_unit_cell_grid=output_box.map_box.all()
print >>log,\
"Output unit cell grid set to: (%s, %s, %s)" %tuple(
output_unit_cell_grid)
expected_output_abc=[]
box_spacing=[]
output_spacing=[]
box_abc=output_box.xray_structure_box.\
crystal_symmetry().unit_cell().parameters()[:3]
if output_crystal_symmetry:
output_abc=output_crystal_symmetry.unit_cell().parameters()[:3]
else:
output_abc=[None,None,None]
for a_box,a_output,n_box,n_output in zip(
box_abc,
output_abc,
output_box.map_box.all(),
output_unit_cell_grid):
expected_output_abc.append(a_box*n_output/n_box)
box_spacing.append(a_box/n_box)
if output_crystal_symmetry:
output_spacing.append(a_output/n_output)
else:
output_spacing.append(a_box/n_box)
if output_crystal_symmetry: # make sure it is compatible...
r0=expected_output_abc[0]/output_abc[0]
r1=expected_output_abc[1]/output_abc[1]
r2=expected_output_abc[2]/output_abc[2]
from libtbx.test_utils import approx_equal
if not approx_equal(r0,r1,eps=0.001) or not approx_equal(r0,r2,eps=0.001):
print >>log,"WARNING: output_unit_cell and cell_grid will "+\
"change ratio of grid spacing.\nOld spacings: "+\
"(%.2f, %.2f, %.2f) A " %(tuple(box_spacing))+\
"\nNew spacings: (%.2f, %.2f, %.2f) A \n" %(tuple(output_spacing))
else:
output_abc=expected_output_abc
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=list(output_abc)+[90,90,90], space_group="P1")
print >>log, \
"Output unit cell will be: (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f)\n"%(
tuple(output_crystal_symmetry.unit_cell().parameters()))
else:
output_unit_cell_grid = map_data=output_box.map_box.all()
output_crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
# ========== Done check/set output unit cell grid and cell parameters =====
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues>0:
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_output_box_output_location.write_pdb_file(file_name=file_name,
crystal_symmetry = output_crystal_symmetry)
print >> log, "Writing boxed PDB with box unit cell to %s" %(
file_name)
# Write NCS file if NCS
if output_box.ncs_object and output_box.ncs_object.max_operators()>0:
if(params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec"%output_prefix
else:
output_symmetry_file = "%s.ncs_spec"%params.output_file_name_prefix
output_box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
print >>log,"\nWriting symmetry to %s" %( output_symmetry_file)
# Write ccp4 map.
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
output_box.write_ccp4_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back)
print >> log, "Writing boxed map "+\
"to CCP4 formatted file: %s"%file_name
# Write xplor map. Shift back if keep_origin=True
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
output_box.write_xplor_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,)
print >> log, "Writing boxed map "+\
"to X-plor formatted file: %s"%file_name
# Write mtz map coeffs. Shift back if keep_origin=True
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print >> log, "Writing map coefficients "+\
"to MTZ file: %s"%file_name
if(map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(map_data=output_box.map_box,
unit_cell=output_box.xray_structure_box.unit_cell())
output_box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor, file_name=file_name,
shift_back=shift_back)
print >> log
return box
def run(
model,
params,
fmodels,
save_optimize_adp_weight,
log,
macro_cycle,
prefix,
target_weights):
target_weights_params = params.target_weights
h_params = params.hydrogens
print_statistics.make_header(prefix, out = log)
if(save_optimize_adp_weight):
r_work = fmodels.fmodel_xray().r_work()
r_free = fmodels.fmodel_xray().r_free()
if ((r_free < r_work or (r_free-r_work)<0.01) and
(not target_weights_params.force_optimize_weights)) :
target_weights_params.optimize_adp_weight = False
else:
target_weights_params.optimize_adp_weight=save_optimize_adp_weight
fmodels.fmodel_xray().xray_structure.scatterers().flags_set_grads(
state = False)
# Exclude H from ADP refinement
if ((params.hydrogens.refine == "riding") or
(params.hydrogens.force_riding_adp)) :
excl_h = model.xray_structure.hd_selection().count(True) > 0
if(excl_h and model.refinement_flags.adp_individual_iso is not None):
model.refinement_flags.adp_individual_iso.set_selected(
model.xray_structure.hd_selection(), False)
if(excl_h and model.refinement_flags.adp_individual_aniso is not None):
model.refinement_flags.adp_individual_aniso.set_selected(
model.xray_structure.hd_selection(), False)
#
save_xray_structure = \
fmodels.fmodel_xray().xray_structure.deep_copy_scatterers() # XXX ?
###> Make ADP of H/D sites equal
model.reset_adp_of_hd_sites_to_be_equal()
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc = True)
tidy_us(params=params, fmodels=fmodels, model=model, log=log)
adp_refinement_manager = adp_refinement.manager(
fmodels = fmodels,
model = model,
group_adp_selections = model.refinement_flags.adp_group,
group_adp_selections_h = model.refinement_flags.group_h,
group_adp_params = params.group_b_iso,
tls_selections = model.refinement_flags.adp_tls,
nm_selections = model.refinement_flags.adp_nm,
all_params = params,
tls_params = params.tls,
nm_params = params.nm,
individual_adp_params = params.adp,
adp_restraints_params = params.adp_restraints,
refine_adp_individual = model.refinement_flags.individual_adp,
refine_adp_group = model.refinement_flags.group_adp,
refine_tls = model.refinement_flags.tls,
refine_nm = model.refinement_flags.nm,
tan_b_iso_max = 0,
restraints_manager = model.restraints_manager,
macro_cycle = macro_cycle,
target_weights = target_weights,
log = log,
h_params = h_params)
assert fmodels.fmodel_xray().xray_structure.min_u_cart_eigenvalue()>=0
print >> log
model.show_adp_statistics(padded = True)
print >> log
fmodels.update_xray_structure(update_f_calc = True)
###> Make ADP of H/D sites equal
model.reset_adp_of_hd_sites_to_be_equal()
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc = True)
assert fmodels.fmodel_xray().xray_structure.min_u_cart_eigenvalue()>=0
def find_tls(params,
pdb_hierarchy,
xray_structure,
return_as_list=False,
ignore_pdb_header_groups=False,
out=None):
"""
!!! WARNING! incoming xray_structure here gets converted to
isotropic B-factors IN PLACE.
"""
if (out is None):
out = sys.stdout
print_statistics.make_header("Analyzing inputs", out=out)
if (params.random_seed is None):
params.random_seed = flex.get_random_seed()
random.seed(params.random_seed)
flex.set_random_seed(params.random_seed)
xray_structure.convert_to_isotropic()
sites_cart = xray_structure.sites_cart()
u_cart = None
u_iso = xray_structure.extract_u_iso_or_u_equiv() #*adptbx.u_as_b(1.) # ?
bad_i_seqs = check_adp(u_iso=u_iso, out=out)
if (bad_i_seqs is not None):
atoms = pdb_hierarchy.atoms()
bad_atom_strings = []
for i_seq in bad_i_seqs[:10]:
atom_str = atoms[i_seq].format_atom_record()
bad_atom_strings.append(atom_str)
if (len(bad_i_seqs) > 10):
bad_atom_strings.append("... (remaining %d not shown)" %
(len(bad_i_seqs) - 10))
raise Sorry(
("%d atoms in the model contain isotropic B-factors <= 0:\n" +
"\n".join(bad_atom_strings)) % (len(bad_i_seqs)))
#
ssm = mmtbx.secondary_structure.manager(pdb_hierarchy=pdb_hierarchy,
sec_str_from_pdb_file=None,
params=None,
log=out)
alpha_h_selection = ssm.helix_selection()
secondary_structure_selection = ssm.helix_selection() | \
ssm.beta_selection() | ssm.base_pair_selection()
if (u_cart is not None):
assert secondary_structure_selection.size() == u_cart.size()
else:
assert secondary_structure_selection.size() == u_iso.size()
ssm.show_summary(log=out)
chains_and_residue_selections, secondary_structure_selection = chains_and_atoms(
pdb_hierarchy=pdb_hierarchy,
secondary_structure_selection=secondary_structure_selection,
out=out)
chains_and_permutations = []
chains_and_atom_selection_strings = []
print_statistics.make_header("Processing chains", out=out)
if (params.nproc is None):
params.nproc = 1
for crs in chains_and_residue_selections:
print_statistics.make_sub_header("Processing chain '%s'" % crs[0],
out=out)
chain_selection = chain_selection_from_residues(crs[1])
groups, perms = get_model_partitioning(
residues=crs[1],
secondary_structure_selection=secondary_structure_selection,
out=out)
#
if (len(perms) == 1):
print(" Whole chain is considered as one TLS group.", file=out)
chains_and_atom_selection_strings.append([
crs[0],
permutations_as_atom_selection_string(groups, perms[0])
])
else:
print(" Fitting TLS matrices...", file=out)
dic = {}
target_best = 1.e+9
if (params.nproc is Auto) or (params.nproc > 1):
process_perms = analyze_permutations(groups=groups,
sites_cart=sites_cart,
u_cart=u_cart,
u_iso=u_iso)
from libtbx import easy_mp
stdout_and_targets = easy_mp.pool_map(
processes=params.nproc,
fixed_func=process_perms,
args=perms,
chunksize=100,
func_wrapper="buffer_stdout_stderr")
targets = [t for so, t in stdout_and_targets]
for (perm, target) in zip(perms, targets):
dic.setdefault(len(perm), []).append([target, perm])
else:
for i_perm, perm in enumerate(perms):
if i_perm % 500 == 0:
print(" ...perm %d of %d" % (i_perm, len(perms)),
file=out)
selections = tls_group_selections(groups, perm)
target = 0
for selection in selections:
mo = tls_refinery(u_cart=u_cart,
u_iso=u_iso,
sites_cart=sites_cart,
selection=selection)
target += mo.f
dic.setdefault(len(perm), []).append([target, perm])
#print " perm %d of %d: target=%8.3f (TLS groups: %s), permutation:"%(
# i_perm, len(perms),target,len(perm)),perm
print(" Best fits:", file=out)
print(" No. of Targets", file=out)
print(" groups best rand.pick diff. score permutation",
file=out)
score_best = -1.e+9
perm_choice = None
for k, v in six.iteritems(dic):
t_best = v[0][0]
perm_best = v[0][1]
for v_ in v:
if (v_[0] < t_best):
t_best = v_[0]
perm_best = v_[1]
if (u_cart is not None):
u_cart_ = u_cart.select(chain_selection)
else:
u_cart_ = None
if (u_iso is not None):
u_iso_ = u_iso.select(chain_selection)
else:
u_iso_ = None
r = tls_refinery_random_groups(
u_cart=u_cart_,
u_iso=u_iso_,
sites_cart=sites_cart.select(chain_selection),
n_groups=k)
score = (r - t_best) / (r + t_best) * 100.
print(" %3d %6.3f %6.3f %6.2f %6.3f" %
(k, t_best, r, r - t_best, score),
perm_best,
file=out)
if (score > score_best):
score_best = score
perm_choice = perm_best[:]
#
chains_and_permutations.append([crs[0], perm_choice])
chains_and_atom_selection_strings.append([
crs[0],
permutations_as_atom_selection_string(groups, perm_choice)
])
#
print_statistics.make_header("SUMMARY", out=out)
#print "Optimal TLS groups:"
#for chain_and_permutation in chains_and_permutations:
# print chain_and_permutation
#print
print("TLS atom selections for phenix.refine:", file=out)
groups_out = StringIO()
selection_strings = []
print("refinement.refine.adp {", file=groups_out)
for r in chains_and_atom_selection_strings:
prefix = "chain '%s'" % r[0]
if (len(r[1]) > 0 and len(r[1:]) > 0):
prefix += " and "
for r_ in r[1:]:
for r__ in r_:
if (len(r__) > 0):
group_selection = prefix + "(%s)" % r__
print(" tls = \"%s\"" % group_selection,
file=groups_out)
selection_strings.append("%s" % group_selection)
else:
print(" tls = \"%s\"" % prefix, file=groups_out)
selection_strings.append("%s" % prefix)
print("}", file=groups_out)
print(groups_out.getvalue(), file=out)
print(file=out)
#XXX
if 0:
merge_groups_by_connectivity(pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
selection_strings=selection_strings)
#XXX
if (len(selection_strings) > 0):
total_target = total_score(pdb_hierarchy=pdb_hierarchy,
sites_cart=sites_cart,
u_iso=u_iso,
selection_strings=selection_strings)
print(
"Overall best total target for automatically found groups: %10.1f"
% total_target,
file=out)
print(file=out)
if (return_as_list):
return selection_strings
else:
return groups_out.getvalue()
def __init__(
self,
fmodels,
model,
params,
target_weights,
macro_cycle,
ncs_manager=None,
log=None):
if log is None:
log = sys.stdout
# self.ncs_manager = ncs_manager
self.nproc = params.main.nproc
if self.nproc is Auto:
self.nproc = 1
self.verbose = params.den.verbose
self.log = log
self.fmodels = fmodels
self.model = model
self.params = params
self.target_weights = target_weights
self.adp_refinement_manager = None
self.macro_cycle = macro_cycle
self.tan_b_iso_max = 0
self.random_seed = params.main.random_seed
den_manager = model.restraints_manager. \
geometry.den_manager
print_statistics.make_header("DEN refinement", out=self.log)
pdb_hierarchy = self.model.get_hierarchy(sync_with_xray_structure=True)
if den_manager.get_n_proxies() == 0:
print_statistics.make_sub_header(
"DEN restraint nework", out = self.log)
den_manager.build_den_proxies(pdb_hierarchy=pdb_hierarchy)
den_manager.build_den_restraints()
den_manager.show_den_summary(
sites_cart=self.model.get_sites_cart())
if den_manager.params.output_kinemage:
den_manager.output_kinemage(
self.model.get_sites_cart())
print_statistics.make_sub_header(
"coordinate minimization before annealing", out=self.log)
self.minimize(ca_only=self.params.den.minimize_c_alpha_only)
self.save_scatterers_local = fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
#DEN refinement start, turn on
if params.den.optimize:
grid = den_manager.get_optimization_grid()
print >> log, \
"Running DEN torsion optimization on %d processors..." % \
params.main.nproc
else:
grid = [(params.den.gamma, params.den.weight)]
grid_results = []
grid_so = []
if "torsion" in params.den.annealing_type:
print >> self.log, "Running torsion simulated annealing"
if ( (params.den.optimize) and
( (self.nproc is Auto) or (self.nproc > 1) )):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_torsion,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError(("DEN weight optimization failed:"+
"\n%s\nThis is a "+
"serious error; please contact [email protected].") % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_torsion(
grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_torsion(grid_results)
elif "cartesian" in params.den.annealing_type:
print >> self.log, "Running Cartesian simulated annealing"
if ( (params.den.optimize) and
( (self.nproc is Auto) or (self.nproc > 1) )):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_cartesian,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError(("DEN weight optimization failed:"+
"\n%s\nThis is a "+
"serious error; please contact [email protected].") % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_cartesian(
grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_cartesian(grid_results)
else:
raise "error in DEN annealing type"
low_r_free = 1.0
best_xray_structure = None
best_eq_distances = None
best_gamma = None
best_weight = None
best_so_i = None
for i, result in enumerate(grid_results):
cur_r_free = result[2]
if cur_r_free < low_r_free:
low_r_free = cur_r_free
best_gamma = result[0]
best_weight = result[1]
best_xray_structure = result[3]
best_eq_distances = result[4]
best_so_i = i
assert best_xray_structure is not None
if params.den.optimize:
print >> self.log, "\nbest gamma: %.1f" % best_gamma
print >> self.log, "best weight: %.1f\n" % best_weight
if params.den.verbose:
if len(grid_so) >= (best_so_i+1):
print >> self.log, "\nBest annealing results:\n"
print >> self.log, grid_so[best_so_i]
fmodels.fmodel_xray().xray_structure.replace_scatterers(
best_xray_structure.deep_copy())
fmodels.update_xray_structure(
xray_structure = fmodels.fmodel_xray().xray_structure,
update_f_calc = True)
utils.assert_xray_structures_equal(
x1 = fmodels.fmodel_xray().xray_structure,
x2 = model.get_xray_structure())
model.restraints_manager.geometry.\
den_manager.import_eq_distances(eq_distances=best_eq_distances)
self.model.torsion_ncs_restraints_update(log=self.log)