def __init__(self, pdbf, mtzf, log):
self.log = log
# Get objects out of files, and set grid step
D = get_data(pdbf, mtzf)
#
print("-" * 79, file=log)
print("A-2013, all defaults", file=log)
step_default = min(0.8, D.f_obs().d_min() / 4)
if (step_default < 0.15): step_default = 0.15
f_mask = mosaic.get_f_mask(xrs=D.xray_structure,
ma=D.f_obs(),
step=step_default)
self.fmodel_2013 = get_fmodel(o=D,
f_mask=f_mask,
remove_outliers=False,
log=self.log).fmodel
#
# Compute masks and F_masks (Mosaic)
print("-" * 79, file=log)
print("Mosaic", file=log)
self.mm = mosaic.mosaic_f_mask(
xray_structure=D.xray_structure,
step=0.6,
volume_cutoff=50,
mean_diff_map_threshold=0.5,
r_sol=1.1, # whole
r_shrink=0.9, # whole
f_obs=self.fmodel_2013.f_obs(),
f_calc=self.fmodel_2013.f_calc(),
log=log)
#
if (self.mm.do_mosaic):
######
print("-" * 79, file=log)
print("A-2013, opt step/radii", file=log)
f_mask_opt = mosaic.get_f_mask(xrs=D.xray_structure,
ma=self.fmodel_2013.f_obs(),
step=0.6,
r_shrink=0.9,
r_sol=1.1)
o = get_fmodel(o=self.fmodel_2013,
f_mask=f_mask_opt,
remove_outliers=False,
log=self.log)
self.fmodel_2013_opt = o.fmodel
self.mc_whole_mask = o.mc
######
print("-" * 79, file=log)
print("A-2013, opt step/radii, using largest mask only", file=log)
o = get_fmodel(o=self.fmodel_2013,
f_mask=self.mm.f_mask_0,
remove_outliers=False,
log=self.log)
self.fmodel_0 = o.fmodel
self.mc_0 = o.mc
def __init__(self, pdbf, mtzf, log, volume_cutoff=30):
self.log = log
# Get objects out of files, and set grid step
D = get_data(pdbf, mtzf)
step = min(0.4, D.f_obs().d_min() / 4)
#
print("-" * 79, file=log)
print("A-2013, all defaults (except set binning)", file=log)
f_mask = mosaic.get_f_mask(xrs=D.xray_structure,
ma=D.f_obs(),
step=D.f_obs().d_min() / 4)
self.fmodel_2013 = get_fmodel(o=D,
f_mask=f_mask,
remove_outliers=True,
log=self.log).fmodel
#
# Compute masks and F_masks (Mosaic)
print("-" * 79, file=log)
print("Mosaic", file=log)
self.mm = mosaic.mosaic_f_mask(xray_structure=D.xray_structure,
step=step,
volume_cutoff=volume_cutoff,
f_obs=self.fmodel_2013.f_obs(),
f_calc=self.fmodel_2013.f_calc(),
log=log)
#
if (self.mm.do_mosaic):
#
print("-" * 79, file=log)
print("A-2013, step=0.4A", file=log)
f_mask_04 = mosaic.get_f_mask(xrs=D.xray_structure,
ma=self.fmodel_2013.f_obs(),
step=step)
o = get_fmodel(o=self.fmodel_2013,
f_mask=f_mask_04,
remove_outliers=False,
log=self.log)
self.fmodel_2013_04 = o.fmodel
self.mc_whole_mask = o.mc
#
self.fmodel_largest_mask = None
self.mc_largest_mask = None
if (self.mm.f_mask_0 is not None):
print("-" * 79, file=log)
print("A-2013, step=0.4A, using largest mask only", file=log)
o = get_fmodel(o=self.fmodel_2013,
f_mask=self.mm.f_mask_0,
remove_outliers=False,
log=self.log)
self.fmodel_largest_mask = o.fmodel
self.mc_largest_mask = o.mc
#
print("-" * 79, file=log)
print(
"A-2013, step=0.4A, filtered mask (no small/negative volumes)",
file=log)
f_mask_fil = self.mm.FV.keys()[0].data()
for fm in self.mm.FV.keys()[1:]:
f_mask_fil = f_mask_fil + fm.data()
f_mask_fil = self.mm.FV.keys()[0].set().array(data=f_mask_fil)
o = get_fmodel(o=self.fmodel_2013,
f_mask=f_mask_fil,
remove_outliers=False,
log=self.log)
self.fmodel_filtered = o.fmodel
self.mc_filtered = o.mc