def run(args=None,params=None,
map_data=None,crystal_symmetry=None,
write_output_files=True,
pdb_inp=None,
ncs_obj=None,
return_map_data_only=False,
return_unshifted_map=False,
half_map_data_list=None,
ncs_copies=None,
n_residues=None,
out=sys.stdout):
# Get the parameters
if not params:
params=get_params(args,out=out)
if not ncs_copies:
ncs_copies=params.crystal_info.ncs_copies
# get map_data and crystal_symmetry
pdb_inp,map_data,half_map_data_list,ncs_obj,crystal_symmetry,acc,\
original_crystal_symmetry,original_unit_cell_grid,map_labels=\
get_map_and_model(
map_data=map_data,
half_map_data_list=half_map_data_list,
pdb_inp=pdb_inp,
ncs_obj=ncs_obj,
map_coords_inside_cell=False,
crystal_symmetry=crystal_symmetry,
get_map_labels=True,
params=params,out=out)
# NOTE: map_data is now relative to origin at (0,0,0).
# Use map_data.reshape(acc) to put it back where it was if acc is not None
# auto-sharpen the map
from cctbx.maptbx.segment_and_split_map import auto_sharpen_map_or_map_coeffs
si=auto_sharpen_map_or_map_coeffs(
resolution=params.crystal_info.resolution, # required
crystal_symmetry=crystal_symmetry,
is_crystal=params.crystal_info.is_crystal,
verbose=params.control.verbose,
resolve_size=params.control.resolve_size,
multiprocessing=params.control.multiprocessing,
nproc=params.control.nproc,
queue_run_command=params.control.queue_run_command,
map=map_data,
half_map_data_list=half_map_data_list,
solvent_content=params.crystal_info.solvent_content,
molecular_mass=params.crystal_info.molecular_mass,
input_weight_map_pickle_file=\
params.input_files.input_weight_map_pickle_file,
output_weight_map_pickle_file=\
params.output_files.output_weight_map_pickle_file,
read_sharpened_maps=params.map_modification.read_sharpened_maps,
write_sharpened_maps=params.map_modification.write_sharpened_maps,
select_sharpened_map=params.map_modification.select_sharpened_map,
auto_sharpen=params.map_modification.auto_sharpen,
local_sharpening=params.map_modification.local_sharpening,
output_directory=params.output_files.output_directory,
smoothing_radius=params.map_modification.smoothing_radius,
local_aniso_in_local_sharpening=\
params.map_modification.local_aniso_in_local_sharpening,
overall_before_local=\
params.map_modification.overall_before_local,
box_in_auto_sharpen=params.map_modification.box_in_auto_sharpen,
density_select_in_auto_sharpen=params.map_modification.density_select_in_auto_sharpen,
density_select_threshold_in_auto_sharpen=params.map_modification.density_select_threshold_in_auto_sharpen,
use_weak_density=params.map_modification.use_weak_density,
discard_if_worse=params.map_modification.discard_if_worse,
box_center=params.map_modification.box_center,
box_size=params.map_modification.box_size,
target_n_overlap=params.map_modification.target_n_overlap,
restrict_map_size=params.map_modification.restrict_map_size,
remove_aniso=params.map_modification.remove_aniso,
auto_sharpen_methods=params.map_modification.auto_sharpen_methods,
residual_target=params.map_modification.residual_target,
region_weight=params.map_modification.region_weight,
sa_percent=params.map_modification.sa_percent,
eps=params.map_modification.eps,
n_bins=params.map_modification.n_bins,
max_regions_to_test=params.map_modification.max_regions_to_test,
regions_to_keep=params.map_modification.regions_to_keep,
fraction_occupied=params.map_modification.fraction_occupied,
sharpening_target=params.map_modification.sharpening_target,
d_min_ratio=params.map_modification.d_min_ratio,
scale_max=params.map_modification.scale_max,
input_d_cut=params.map_modification.input_d_cut,
b_blur_hires=params.map_modification.b_blur_hires,
max_box_fraction=params.map_modification.max_box_fraction,
cc_cut=params.map_modification.cc_cut,
max_cc_for_rescale=params.map_modification.max_cc_for_rescale,
scale_using_last=params.map_modification.scale_using_last,
density_select_max_box_fraction=params.map_modification.density_select_max_box_fraction,
mask_atoms=params.map_modification.mask_atoms,
mask_atoms_atom_radius=params.map_modification.mask_atoms_atom_radius,
value_outside_atoms=params.map_modification.value_outside_atoms,
k_sharpen=params.map_modification.k_sharpen,
optimize_b_blur_hires=params.map_modification.optimize_b_blur_hires,
iterate=params.map_modification.iterate,
optimize_d_cut=params.map_modification.optimize_d_cut,
soft_mask=params.map_modification.soft_mask,
allow_box_if_b_iso_set=params.map_modification.allow_box_if_b_iso_set,
search_b_min=params.map_modification.search_b_min,
search_b_max=params.map_modification.search_b_max,
search_b_n=params.map_modification.search_b_n,
adjust_region_weight=params.map_modification.adjust_region_weight,
region_weight_method=params.map_modification.region_weight_method,
region_weight_factor=params.map_modification.region_weight_factor,
region_weight_buffer=\
params.map_modification.region_weight_buffer,
target_b_iso_ratio=params.map_modification.target_b_iso_ratio,
signal_min=params.map_modification.signal_min,
buffer_radius=params.crystal_info.buffer_radius,
wang_radius=params.crystal_info.wang_radius,
pseudo_likelihood=params.crystal_info.pseudo_likelihood,
target_b_iso_model_scale=params.map_modification.target_b_iso_model_scale,
b_iso=params.map_modification.b_iso,
b_sharpen=params.map_modification.b_sharpen,
resolution_dependent_b=\
params.map_modification.resolution_dependent_b,
normalize_amplitudes_in_resdep=\
params.map_modification.normalize_amplitudes_in_resdep,
pdb_inp=pdb_inp,
ncs_obj=ncs_obj,
rmsd=params.map_modification.rmsd,
rmsd_resolution_factor=params.map_modification.rmsd_resolution_factor,
b_sol=params.map_modification.b_sol,
k_sol=params.map_modification.k_sol,
fraction_complete=params.map_modification.fraction_complete,
seq_file=params.input_files.seq_file,
ncs_copies=ncs_copies,
n_residues=n_residues,
out=out)
# get map_data and map_coeffs of final map
new_map_data=si.as_map_data()
new_map_coeffs=si.as_map_coeffs()
from cctbx.maptbx.segment_and_split_map import get_b_iso,map_coeffs_as_fp_phi
f,phi=map_coeffs_as_fp_phi(new_map_coeffs)
temp_b_iso=get_b_iso(f,d_min=params.crystal_info.resolution)
if not si.is_model_sharpening():
print >>out
print >>out,80*"=","\n",80*"="
print >>out,"\n Summary of sharpening information\n "
si.show_summary(verbose=params.control.verbose,out=out)
print >>out,80*"=","\n",80*"="
# write out the new map_coeffs and map if requested:
offset_map_data=new_map_data.deep_copy()
if acc is not None: # offset the map to match original if possible
offset_map_data.reshape(acc)
if write_output_files and params.output_files.sharpened_map_file and \
offset_map_data:
output_map_file=os.path.join(params.output_files.output_directory,
params.output_files.sharpened_map_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
if acc is not None: # we offset the map to match original
print >>out,\
"\nWrote sharpened map in original location with origin at %s\nto %s" %(
str(offset_map_data.origin()),output_map_file)
write_ccp4_map(original_crystal_symmetry, output_map_file,
offset_map_data,
output_unit_cell_grid=original_unit_cell_grid)
else:
print >>out,"\nWrote sharpened map with origin at 0,0,0 "+\
"(NOTE: may be boxed map and may not be "+\
"\nsame as original location) to %s\n" %(
output_map_file)
from iotbx.mrcfile import create_output_labels
program_name='auto_sharpen'
limitations=["map_is_sharpened"]
labels=create_output_labels(program_name=program_name,
input_file_name=params.input_files.map_file,
input_labels=map_labels,
limitations=limitations,
output_labels=None)
write_ccp4_map(crystal_symmetry, output_map_file, offset_map_data,
labels=labels)
if write_output_files and params.output_files.shifted_sharpened_map_file:
output_map_file=os.path.join(params.output_files.output_directory,
params.output_files.shifted_sharpened_map_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
write_ccp4_map(crystal_symmetry, output_map_file, new_map_data)
print >>out,"\nWrote sharpened map (origin at %s)\nto %s" %(
str(new_map_data.origin()),output_map_file)
if write_output_files and params.output_files.sharpened_map_coeffs_file and \
new_map_coeffs:
output_map_coeffs_file=os.path.join(params.output_files.output_directory,
params.output_files.sharpened_map_coeffs_file)
new_map_coeffs.as_mtz_dataset(column_root_label='FWT').mtz_object().write(
file_name=output_map_coeffs_file)
print >>out,"\nWrote sharpened map_coeffs (origin at 0,0,0)\n to %s\n" %(
output_map_coeffs_file)
if return_unshifted_map:
map_to_return=offset_map_data
else:
map_to_return=new_map_data
if return_map_data_only:
return map_to_return
else: #usual
return map_to_return,new_map_coeffs,crystal_symmetry,si
def run(args=None,
params=None,
map_data=None,
crystal_symmetry=None,
write_output_files=True,
pdb_inp=None,
ncs_obj=None,
return_map_data_only=False,
half_map_data_list=None,
ncs_copies=None,
n_residues=None,
out=sys.stdout):
# Get the parameters
if not params:
params = get_params(args, out=out)
if not ncs_copies:
ncs_copies = params.crystal_info.ncs_copies
# get map_data and crystal_symmetry
pdb_inp,map_data,half_map_data_list,ncs_obj,\
crystal_symmetry,acc=get_map_and_model(
map_data=map_data,
half_map_data_list=half_map_data_list,
pdb_inp=pdb_inp,
ncs_obj=ncs_obj,
crystal_symmetry=crystal_symmetry,
params=params,out=out)
# NOTE: map_data is now relative to origin at (0,0,0).
# Use map_data.reshape(acc) to put it back where it was if acc is not None
# auto-sharpen the map
from cctbx.maptbx.segment_and_split_map import auto_sharpen_map_or_map_coeffs
si=auto_sharpen_map_or_map_coeffs(
resolution=params.crystal_info.resolution, # required
crystal_symmetry=crystal_symmetry,
is_crystal=params.crystal_info.is_crystal,
verbose=params.control.verbose,
map=map_data,
half_map_data_list=half_map_data_list,
solvent_content=params.crystal_info.solvent_content,
input_weight_map_pickle_file=\
params.input_files.input_weight_map_pickle_file,
output_weight_map_pickle_file=\
params.output_files.output_weight_map_pickle_file,
read_sharpened_maps=params.map_modification.read_sharpened_maps,
write_sharpened_maps=params.map_modification.write_sharpened_maps,
select_sharpened_map=params.map_modification.select_sharpened_map,
auto_sharpen=params.map_modification.auto_sharpen,
local_sharpening=params.map_modification.local_sharpening,
output_directory=params.output_files.output_directory,
smoothing_radius=params.map_modification.smoothing_radius,
local_aniso_in_local_sharpening=\
params.map_modification.local_aniso_in_local_sharpening,
box_in_auto_sharpen=params.map_modification.box_in_auto_sharpen,
use_weak_density=params.map_modification.use_weak_density,
discard_if_worse=params.map_modification.discard_if_worse,
box_center=params.map_modification.box_center,
box_size=params.map_modification.box_size,
remove_aniso=params.map_modification.remove_aniso,
auto_sharpen_methods=params.map_modification.auto_sharpen_methods,
residual_target=params.map_modification.residual_target,
region_weight=params.map_modification.region_weight,
sa_percent=params.map_modification.sa_percent,
eps=params.map_modification.eps,
n_bins=params.map_modification.n_bins,
max_regions_to_test=params.map_modification.max_regions_to_test,
fraction_occupied=params.map_modification.fraction_occupied,
sharpening_target=params.map_modification.sharpening_target,
d_min_ratio=params.map_modification.d_min_ratio,
max_box_fraction=params.map_modification.max_box_fraction,
mask_atoms=params.map_modification.mask_atoms,
mask_atoms_atom_radius=params.map_modification.mask_atoms_atom_radius,
value_outside_atoms=params.map_modification.value_outside_atoms,
k_sharpen=params.map_modification.k_sharpen,
soft_mask=params.map_modification.soft_mask,
search_b_min=params.map_modification.search_b_min,
search_b_max=params.map_modification.search_b_max,
search_b_n=params.map_modification.search_b_n,
maximum_low_b_adjusted_sa=\
params.map_modification.maximum_low_b_adjusted_sa,
b_iso=params.map_modification.b_iso,
b_sharpen=params.map_modification.b_sharpen,
resolution_dependent_b=\
params.map_modification.resolution_dependent_b,
pdb_inp=pdb_inp,
ncs_obj=ncs_obj,
rmsd=params.map_modification.rmsd,
b_sol=params.map_modification.b_sol,
k_sol=params.map_modification.k_sol,
fraction_complete=params.map_modification.fraction_complete,
seq_file=params.input_files.seq_file,
ncs_copies=ncs_copies,
n_residues=n_residues,
out=out)
# get map_data and map_coeffs of final map
new_map_data = si.as_map_data()
new_map_coeffs = si.as_map_coeffs()
from cctbx.maptbx.segment_and_split_map import get_b_iso, map_coeffs_as_fp_phi
f, phi = map_coeffs_as_fp_phi(new_map_coeffs)
temp_b_iso = get_b_iso(f, d_min=params.crystal_info.resolution)
if not si.is_model_sharpening():
print >> out
print >> out, 80 * "=", "\n", 80 * "="
print >> out, "\n Summary of sharpening information\n "
si.show_summary(verbose=params.control.verbose, out=out)
print >> out, 80 * "=", "\n", 80 * "="
# write out the new map_coeffs and map if requested:
if write_output_files and params.output_files.sharpened_map_file and \
new_map_data:
output_map_file = os.path.join(params.output_files.output_directory,
params.output_files.sharpened_map_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
offset_map_data = new_map_data.deep_copy()
if acc is not None: # offset the map to match original if possible
offset_map_data.reshape(acc)
print >>out,\
"\nWrote sharpened map in original location with origin at %s\nto %s" %(
str(offset_map_data.origin()),output_map_file)
else:
print >>out,"\nWrote sharpened map with origin at 0,0,0 "+\
"(NOTE: may not be \nsame as original location) to %s\n" %(
output_map_file)
write_ccp4_map(crystal_symmetry, output_map_file, offset_map_data)
if write_output_files and params.output_files.shifted_sharpened_map_file:
output_map_file = os.path.join(
params.output_files.output_directory,
params.output_files.shifted_sharpened_map_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
write_ccp4_map(crystal_symmetry, output_map_file, new_map_data)
print >> out, "\nWrote sharpened map (origin at %s)\nto %s" % (str(
new_map_data.origin()), output_map_file)
if write_output_files and params.output_files.sharpened_map_coeffs_file and \
new_map_coeffs:
output_map_coeffs_file = os.path.join(
params.output_files.output_directory,
params.output_files.sharpened_map_coeffs_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
new_map_coeffs.as_mtz_dataset(
column_root_label='FWT').mtz_object().write(
file_name=output_map_coeffs_file)
print >> out, "\nWrote sharpened map_coeffs (origin at 0,0,0)\n to %s\n" % (
output_map_coeffs_file)
if return_map_data_only:
return new_map_data
else: #usual
return new_map_data, new_map_coeffs, crystal_symmetry, si
def run(args, out=sys.stdout):
# Get the parameters
params = get_params(args, out=out)
# get map_data and crystal_symmetry
map_data, crystal_symmetry = get_map(params=params, out=out)
# auto-sharpen the map
from cctbx.maptbx.segment_and_split_map import auto_sharpen_map_or_map_coeffs
new_map_data=auto_sharpen_map_or_map_coeffs(
resolution=params.crystal_info.resolution, # required
crystal_symmetry=crystal_symmetry,
map=map_data,
solvent_content=params.crystal_info.solvent_content,
box_in_auto_sharpen=params.map_modification.box_in_auto_sharpen,
auto_sharpen_methods=params.map_modification.auto_sharpen_methods,
residual_target=params.map_modification.residual_target,
region_weight=params.map_modification.region_weight,
sa_percent=params.map_modification.sa_percent,
eps=params.map_modification.eps,
n_bins=params.map_modification.n_bins,
max_regions_to_test=params.map_modification.max_regions_to_test,
fraction_occupied=params.map_modification.fraction_occupied,
sharpening_target=params.map_modification.sharpening_target,
d_min_ratio=params.map_modification.d_min_ratio,
max_box_fraction=params.map_modification.max_box_fraction,
k_sharpen=params.map_modification.max_box_fraction,
search_b_min=params.map_modification.search_b_min,
search_b_max=params.map_modification.search_b_max,
search_b_n=params.map_modification.search_b_n,
b_iso=params.map_modification.b_iso,
b_sharpen=params.map_modification.b_sharpen,
resolution_dependent_b=\
params.map_modification.resolution_dependent_b,
out=out)
# convert to map_coeffs also
from cctbx.maptbx.segment_and_split_map import get_f_phases_from_map
new_map_coeffs = get_f_phases_from_map(
map_data=new_map_data,
crystal_symmetry=crystal_symmetry,
d_min=params.crystal_info.resolution,
d_min_ratio=params.map_modification.d_min_ratio,
return_as_map_coeffs=True,
out=out)
# write out the new map_coeffs and map if requested:
if params.output_files.shifted_sharpened_map_file:
output_map_file = os.path.join(
params.output_files.output_directory,
params.output_files.shifted_sharpened_map_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
write_ccp4_map(crystal_symmetry, output_map_file, new_map_data)
print >> out, "\nWrote sharpened map to %s" % (output_map_file)
if params.output_files.shifted_sharpened_map_coeffs_file:
output_map_coeffs_file = os.path.join(
params.output_files.output_directory,
params.output_files.shifted_sharpened_map_coeffs_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
new_map_coeffs.as_mtz_dataset(
column_root_label='FWT').mtz_object().write(
file_name=output_map_coeffs_file)
print >> out, "\nWrote sharpened map_coeffs to %s" % (
output_map_coeffs_file)
return new_map_data, new_map_coeffs, crystal_symmetry
def run(args,out=sys.stdout):
# Get the parameters
params=get_params(args,out=out)
# get map_data and crystal_symmetry
map_data,crystal_symmetry=get_map(params=params,out=out)
# auto-sharpen the map
from cctbx.maptbx.segment_and_split_map import auto_sharpen_map_or_map_coeffs
new_map_data=auto_sharpen_map_or_map_coeffs(
resolution=params.crystal_info.resolution, # required
crystal_symmetry=crystal_symmetry,
map=map_data,
solvent_content=params.crystal_info.solvent_content,
box_in_auto_sharpen=params.map_modification.box_in_auto_sharpen,
auto_sharpen_methods=params.map_modification.auto_sharpen_methods,
residual_target=params.map_modification.residual_target,
region_weight=params.map_modification.region_weight,
sa_percent=params.map_modification.sa_percent,
eps=params.map_modification.eps,
n_bins=params.map_modification.n_bins,
max_regions_to_test=params.map_modification.max_regions_to_test,
fraction_occupied=params.map_modification.fraction_occupied,
sharpening_target=params.map_modification.sharpening_target,
d_min_ratio=params.map_modification.d_min_ratio,
max_box_fraction=params.map_modification.max_box_fraction,
k_sharpen=params.map_modification.max_box_fraction,
search_b_min=params.map_modification.search_b_min,
search_b_max=params.map_modification.search_b_max,
search_b_n=params.map_modification.search_b_n,
b_iso=params.map_modification.b_iso,
b_sharpen=params.map_modification.b_sharpen,
resolution_dependent_b=\
params.map_modification.resolution_dependent_b,
out=out)
# convert to map_coeffs also
from cctbx.maptbx.segment_and_split_map import get_f_phases_from_map
new_map_coeffs=get_f_phases_from_map(map_data=new_map_data,
crystal_symmetry=crystal_symmetry,
d_min=params.crystal_info.resolution,
d_min_ratio=params.map_modification.d_min_ratio,
return_as_map_coeffs=True,
out=out)
# write out the new map_coeffs and map if requested:
if params.output_files.shifted_sharpened_map_file:
output_map_file=os.path.join(params.output_files.output_directory,
params.output_files.shifted_sharpened_map_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
write_ccp4_map(crystal_symmetry, output_map_file, new_map_data)
print >>out,"\nWrote sharpened map to %s" %(output_map_file)
if params.output_files.shifted_sharpened_map_coeffs_file:
output_map_coeffs_file=os.path.join(params.output_files.output_directory,
params.output_files.shifted_sharpened_map_coeffs_file)
from cctbx.maptbx.segment_and_split_map import write_ccp4_map
new_map_coeffs.as_mtz_dataset(column_root_label='FWT').mtz_object().write(
file_name=output_map_coeffs_file)
print >>out,"\nWrote sharpened map_coeffs to %s" %(output_map_coeffs_file)
return new_map_data,new_map_coeffs,crystal_symmetry
