def map_coefficients_from_fmodel(
params,
fmodel = None,
map_calculation_server = None,
post_processing_callback=None,
pdb_hierarchy=None):
assert [fmodel, map_calculation_server].count(None) == 1
from mmtbx import map_tools
import mmtbx
from cctbx import miller
mnm = mmtbx.map_names(map_name_string = params.map_type)
if(mnm.k==0 and abs(mnm.n)==1):
# FIXME Fcalc maps require that fmodel is not None!
if (fmodel is None) :
fmodel = map_calculation_server.fmodel
return compute_f_calc(fmodel, params)
if(fmodel is not None and
fmodel.is_twin_fmodel_manager() and
mnm.phaser_sad_llg):
return None
if(fmodel is not None):
e_map_obj = fmodel.electron_density_map()
xrs = fmodel.xray_structure
else:
e_map_obj = map_calculation_server
xrs = map_calculation_server.fmodel.xray_structure
coeffs = None
coeffs = e_map_obj.map_coefficients(
map_type = params.map_type,
acentrics_scale = params.acentrics_scale,
centrics_pre_scale = params.centrics_pre_scale,
fill_missing = params.fill_missing_f_obs,
isotropize = params.isotropize,
exclude_free_r_reflections=params.exclude_free_r_reflections,
ncs_average=getattr(params, "ncs_average", False),
post_processing_callback=post_processing_callback,
pdb_hierarchy=pdb_hierarchy,
merge_anomalous=True)
if (coeffs is None) : return None
if(params.sharpening):
from mmtbx import map_tools
coeffs, b_sharp = map_tools.sharp_map(
sites_frac = xrs.sites_frac(),
map_coeffs = coeffs,
b_sharp = params.sharpening_b_factor)
# XXX need to figure out why this happens
if (coeffs is None) :
raise RuntimeError(("Map coefficient generation failed (map_type=%s, "
"sharpening=%s, isotropize=%s, anomalous=%s.") %
(params.map_type, params.sharpening, params.isotropize,
fmodel.f_obs().anomalous_flag()))
if(coeffs.anomalous_flag()) :
coeffs = coeffs.average_bijvoet_mates()
return coeffs
def run (args, out=sys.stdout) :
master_params = master_phil()
usage_string = """\
mmtbx.compute_map_coefficients model.pdb data.mtz map_type=MAP_TYPE [options]
Utility to compute a single set of map coefficients with minimal input.
"""
import mmtbx.command_line
from mmtbx import map_tools
import iotbx.mtz
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_params,
process_pdb_file=False,
prefer_anomalous=True,
usage_string=usage_string,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
out=out)
fmodel = cmdline.fmodel
xray_structure = fmodel.xray_structure
params = cmdline.params
map_coeffs = fmodel.map_coefficients(
map_type=params.map_type,
exclude_free_r_reflections=params.exclude_free_r_reflections,
fill_missing=params.fill_missing_f_obs)
if (params.b_sharp is not None) :
if (params.b_sharp is Auto) :
params.b_sharp = - map_coeffs.d_min() * 10
map_coeffs = map_tools.sharp_map(
sites_frac=None,
map_coeffs=map_coeffs,
b_sharp=b_sharp)
dec = iotbx.mtz.label_decorator(phases_prefix="PH")
mtz_dataset = map_coeffs.as_mtz_dataset(
column_root_label=map_type_labels[params.map_type],
label_decorator=dec)
if (params.output_file is Auto) :
pdb_file = os.path.basename(params.input.pdb.file_name[0])
params.output_file = os.path.splitext(pdb_file)[0] + "_%s.mtz" % \
params.map_type
mtz_dataset.mtz_object().write(params.output_file)
print >> out, "Wrote %s" % params.output_file
def run(args, out=sys.stdout):
master_params = master_phil()
usage_string = """\
mmtbx.compute_map_coefficients model.pdb data.mtz map_type=MAP_TYPE [options]
Utility to compute a single set of map coefficients with minimal input.
"""
import mmtbx.command_line
from mmtbx import map_tools
import iotbx.mtz
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_params,
process_pdb_file=False,
prefer_anomalous=True,
usage_string=usage_string,
set_wavelength_from_model_header=True,
set_inelastic_form_factors="sasaki",
out=out)
fmodel = cmdline.fmodel
xray_structure = fmodel.xray_structure
params = cmdline.params
map_coeffs = fmodel.map_coefficients(
map_type=params.map_type,
exclude_free_r_reflections=params.exclude_free_r_reflections,
fill_missing=params.fill_missing_f_obs)
if (params.b_sharp is not None):
if (params.b_sharp is Auto):
params.b_sharp = - map_coeffs.d_min() * 10
map_coeffs = map_tools.sharp_map(
sites_frac=None,
map_coeffs=map_coeffs,
b_sharp=b_sharp)
dec = iotbx.mtz.label_decorator(phases_prefix="PH")
mtz_dataset = map_coeffs.as_mtz_dataset(
column_root_label=map_type_labels[params.map_type],
label_decorator=dec)
if (params.output_file is Auto):
pdb_file = os.path.basename(params.input.pdb.file_name[0])
params.output_file = os.path.splitext(pdb_file)[0] + "_%s.mtz" % \
params.map_type
mtz_dataset.mtz_object().write(params.output_file)
print("Wrote %s" % params.output_file, file=out)
