def get_model_map_coeffs_normalized(pdb_inp=None,
si=None,
f_array=None,
overall_b=None,
resolution=None,
n_bins=None,
target_b_iso_model_scale=0,
out=sys.stdout):
if not pdb_inp: return None
if not si:
from cctbx.maptbx.segment_and_split_map import sharpening_info
si=sharpening_info(resolution=resolution,
target_b_iso_model_scale=0,
n_bins=n_bins)
# define Wilson B for the model
if overall_b is None:
if si.resolution:
overall_b=si.get_target_b_iso()*si.target_b_iso_model_scale
else:
overall_b=0
print("Setting Wilson B = %5.1f A" %(overall_b), file=out)
# create model map using same coeffs
from cctbx.maptbx.segment_and_split_map import get_f_phases_from_model
try:
model_map_coeffs=get_f_phases_from_model(
pdb_inp=pdb_inp,
f_array=f_array,
overall_b=overall_b,
k_sol=si.k_sol,
b_sol=si.b_sol,
out=out)
except Exception as e:
print ("Failed to get model map coeffs...going on",file=out)
return None
from cctbx.maptbx.segment_and_split_map import map_coeffs_as_fp_phi,get_b_iso
model_f_array,model_phases=map_coeffs_as_fp_phi(model_map_coeffs)
(d_max,d_min)=f_array.d_max_min()
model_f_array.setup_binner(n_bins=si.n_bins,d_max=d_max,d_min=d_min)
# Set overall_b....
final_b_iso=get_b_iso(model_f_array,d_min=resolution)
print("Effective b_iso of "+\
"adjusted model map: %6.1f A**2" %(final_b_iso), file=out)
model_map_coeffs_normalized=model_f_array.phase_transfer(
phase_source=model_phases,deg=True)
return model_map_coeffs_normalized
def get_model_map_coeffs_normalized(pdb_inp=None,
si=None,
f_array=None,
overall_b=None,
resolution=None,
out=sys.stdout):
if not pdb_inp: return None
# define Wilson B for the model
if overall_b is None:
overall_b = 10 * resolution
print >> out, "Setting Wilson B = %5.1f A based on resolution of %5.1f A" % (
overall_b, resolution)
# create model map using same coeffs
from cctbx.maptbx.segment_and_split_map import get_f_phases_from_model
model_map_coeffs = get_f_phases_from_model(pdb_inp=pdb_inp,
f_array=f_array,
overall_b=overall_b,
k_sol=si.k_sol,
b_sol=si.b_sol,
out=out)
from cctbx.maptbx.segment_and_split_map import map_coeffs_as_fp_phi, get_b_iso
model_f_array, model_phases = map_coeffs_as_fp_phi(model_map_coeffs)
(d_max, d_min) = f_array.d_max_min()
model_f_array.setup_binner(n_bins=si.n_bins, d_max=d_max, d_min=d_min)
# Set overall_b....
starting_b_iso = get_b_iso(model_f_array, d_min=resolution)
model_f_array=\
model_f_array.apply_debye_waller_factors(
b_iso=overall_b-starting_b_iso)
final_b_iso = get_b_iso(model_f_array, d_min=resolution)
print >>out,"Effective b_iso of initial and "+\
"adjusted model map: %6.1f A**2 %6.1f A**2" %(starting_b_iso,final_b_iso)
model_map_coeffs_normalized = model_f_array.phase_transfer(
phase_source=model_phases, deg=True)
return model_map_coeffs_normalized