def check_refinement_stability(self):
if not self.shall_refine_thermal_displacements:
for sc in self.xray_structure.scatterers():
sc.flags.set_grad_site(True)
if sc.flags.use_u_aniso(): sc.flags.set_grad_u_aniso(False)
if sc.flags.use_u_iso(): sc.flags.set_grad_u_iso(False)
xs = self.xray_structure
xs0 = self.reference_xray_structure = xs.deep_copy_scatterers()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
xs.shake_sites_in_place(rms_difference=0.1)
if self.shall_refine_thermal_displacements:
# a spread of 10 for u_iso's would be enormous for our low temperature
# test structures if those u_iso's were not constrained
xs.shake_adp(
spread=10, # absolute
aniso_spread=0.2) # relative
self.reparametrisation = constraints.reparametrisation(
xs,
self.constraints,
self.connectivity_table,
temperature=self.t_celsius)
obs = fo_sq.as_xray_observations()
ls = least_squares.crystallographic_ls(
obs,
self.reparametrisation,
weighting_scheme=least_squares.mainstream_shelx_weighting())
self.cycles = self.normal_eqns_solving_method(ls)
print("%i %s iterations to recover from shaking" %
(self.cycles.n_iterations, self.cycles))
if 0:
from crys3d.qttbx.xray_structure_viewer import display
display(xray_structure=xs)
diff = xray.meaningful_site_cart_differences(xs0, xs)
assert diff.max_absolute() < self.site_refinement_tolerance,\
self.__class__.__name__
if self.shall_refine_thermal_displacements:
delta_u = []
for sc, sc0 in itertools.izip(xs.scatterers(), xs0.scatterers()):
if not sc.flags.use_u_aniso() or not sc0.flags.use_u_aniso():
continue
delta_u.extend(matrix.col(sc.u_star) - matrix.col(sc0.u_star))
delta_u = flex.double(delta_u)
assert flex.max_absolute(delta_u) < self.u_star_refinement_tolerance,\
self.__class__.__name__
def check_refinement_stability(self):
if not self.shall_refine_thermal_displacements:
for sc in self.xray_structure.scatterers():
sc.flags.set_grad_site(True)
if sc.flags.use_u_aniso(): sc.flags.set_grad_u_aniso(False)
if sc.flags.use_u_iso(): sc.flags.set_grad_u_iso(False)
xs = self.xray_structure
xs0 = self.reference_xray_structure = xs.deep_copy_scatterers()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
xs.shake_sites_in_place(rms_difference=0.1)
if self.shall_refine_thermal_displacements:
# a spread of 10 for u_iso's would be enormous for our low temperature
# test structures if those u_iso's were not constrained
xs.shake_adp(spread=10, # absolute
aniso_spread=0.2) # relative
self.reparametrisation = constraints.reparametrisation(
xs, self.constraints, self.connectivity_table,
temperature=self.t_celsius)
obs = fo_sq.as_xray_observations()
ls = least_squares.crystallographic_ls(
obs,
self.reparametrisation,
weighting_scheme=least_squares.mainstream_shelx_weighting())
self.cycles = self.normal_eqns_solving_method(ls)
print ("%i %s iterations to recover from shaking"
% (self.cycles.n_iterations,
self.cycles))
if 0:
from crys3d.qttbx.xray_structure_viewer import display
display(xray_structure=xs)
diff = xray.meaningful_site_cart_differences(xs0, xs)
assert diff.max_absolute() < self.site_refinement_tolerance,\
self.__class__.__name__
if self.shall_refine_thermal_displacements:
delta_u = []
for sc, sc0 in itertools.izip(xs.scatterers(), xs0.scatterers()):
if not sc.flags.use_u_aniso() or not sc0.flags.use_u_aniso(): continue
delta_u.extend(matrix.col(sc.u_star) - matrix.col(sc0.u_star))
delta_u = flex.double(delta_u)
assert flex.max_absolute(delta_u) < self.u_star_refinement_tolerance,\
self.__class__.__name__
def display_structure(self):
from crys3d.qttbx.xray_structure_viewer import display
display(xray_structure=self.xray_structure)
def display_structure(self): from crys3d.qttbx.xray_structure_viewer import display display(xray_structure=self.xray_structure)
from __future__ import absolute_import, division, print_function
from cctbx import xray
from crys3d.qttbx import xray_structure_viewer
try:
import durham_structures
except ImportError:
durham_structures = None
import sys, os
name = sys.argv[1]
filename = os.path.expanduser(name)
if os.path.exists(filename):
xs = xray.structure.from_shelx(filename=filename, strictly_shelxl=False)
elif durham_structures:
xs = durham_structures.some([name]).next().xray_structure
else:
print("%s not found" % name)
sys.exit(1)
xray_structure_viewer.display(xray_structure=xs, name=name)
from __future__ import division from cctbx import xray from crys3d.qttbx import xray_structure_viewer try: import durham_structures except ImportError: durham_structures = None import sys, os name = sys.argv[1] filename = os.path.expanduser(name) if os.path.exists(filename): xs = xray.structure.from_shelx(filename=filename, strictly_shelxl=False) elif durham_structures: xs = durham_structures.some([name]).next().xray_structure else: print "%s not found" % name sys.exit(1) xray_structure_viewer.display(xray_structure=xs, name=name)
