def generate_map_coefficients(
model=None, # Required model
output_map_coeffs_file_name=None,
d_min=3,
scattering_table='electron',
log=sys.stdout):
'''
Convenience function to create map coefficients from a model.
This function typically accessed and tested through map_model_manager
Summary: Supply model.manager object or parameters for generate_model,
high_resolution limit of d_min and optional scattering_table ("electron"
for cryo-EM, "n_gaussian" for x-ray) and optional
output_map_coeffs_file_name.
Writes map coefficients and returns miller_array object
containing the map coefficients
Parameters:
-----------
model (model.manager object, None): model to use
output_map_coeffs_file_name (string, None): output model file name
d_min (float, 3): High-resolution limit for map coeffs (A)
scattering_table (choice, 'electron'): choice of scattering table
All choices: wk1995 it1992 n_gaussian neutron electron
'''
assert model is not None
# get map coefficients
from mmtbx.utils import fmodel_from_xray_structure
import iotbx.phil
from mmtbx.command_line.fmodel import master_phil
fmodel_params = master_phil.extract()
assert model.crystal_symmetry(
) is not None # Need crystal_symmetry in model
xrs = model.get_xray_structure()
fmodel_params.high_resolution = float(d_min)
fmodel_params.scattering_table = scattering_table
fmodel = fmodel_from_xray_structure(xray_structure=xrs,
params=fmodel_params,
out=log)
f_model = fmodel.f_model
if output_map_coeffs_file_name:
f_model.as_mtz_dataset(column_root_label='FWT').mtz_object().write(
file_name=output_map_coeffs_file_name)
print("Writing map coefficients to resolution of %s A to %s" %
(d_min, output_map_coeffs_file_name),
file=log)
else:
print("Generated map coefficients to resolution of %s A " % (d_min),
file=log)
return f_model
def generate_map_coefficients(model=None,
output_map_coeffs_file_name=None,
high_resolution=3,
scattering_table='electron',
log=sys.stdout,
**pass_through_kw):
'''
generate_map_coefficients Convenience function to create
map coefficients from a model. Supply model.manager object,
high_resolution limit and optional scattering_table ("electron"
for cryo-EM, "n_gaussian" for x-ray) and optional
output_map_coeffs_file_name.
Writes map coefficients and returns miller_array object
containing the map
'''
if not model:
model = generate_model(log=log, **pass_through_kw)
# get map coefficients
from mmtbx.utils import fmodel_from_xray_structure
import iotbx.phil
from mmtbx.command_line.fmodel import master_phil
fmodel_params = master_phil.extract()
xrs = model.get_xray_structure()
fmodel_params.high_resolution = float(high_resolution)
fmodel_params.scattering_table = scattering_table
fmodel = fmodel_from_xray_structure(xray_structure=xrs,
params=fmodel_params,
out=log)
f_model = fmodel.f_model
if output_map_coeffs_file_name:
f_model.as_mtz_dataset(column_root_label='FWT').mtz_object().write(
file_name=output_map_coeffs_file_name)
print("Writing map coefficients to resolution of %s A to %s" %
(high_resolution, output_map_coeffs_file_name),
file=log)
else:
print("Generated map coefficients to resolution of %s A " %
(high_resolution),
file=log)
return f_model