def refine(self, weight, sites_cart=None, xray_structure=None):
assert xray_structure is not None and [sites_cart,xray_structure].count(None)==1
self.refined = real_space_target_and_gradients.minimization(
xray_structure = xray_structure,
miller_array = self.miller_array,
crystal_gridding = self.crystal_gridding,
map_target = self.map_target,
max_iterations = self.max_iterations,
min_iterations = self.min_iterations,
step = self.step,
real_space_target_weight = weight,
restraints_target_weight = self.restraints_target_weight,
geometry_restraints_manager = self.geometry_restraints_manager,
target_type = "diff_map")
def refine(self, weight, sites_cart=None, xray_structure=None):
assert xray_structure is not None and [sites_cart,xray_structure].count(None)==1
self.refined = real_space_target_and_gradients.minimization(
xray_structure = xray_structure,
miller_array = self.miller_array,
crystal_gridding = self.crystal_gridding,
map_target = self.map_target,
max_iterations = self.max_iterations,
min_iterations = self.min_iterations,
step = self.step,
real_space_target_weight = weight,
restraints_target_weight = self.restraints_target_weight,
geometry_restraints_manager = self.geometry_restraints_manager,
target_type = "diff_map")
def run():
def compute_map(xray_structure, d_min=1.5, resolution_factor=1. / 4):
fc = xray_structure.structure_factors(d_min=d_min).f_calc()
fft_map = fc.fft_map(resolution_factor=resolution_factor)
fft_map.apply_sigma_scaling()
result = fft_map.real_map_unpadded()
return result, fc, fft_map
xrs = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("P212121"),
elements=["N", "C", "O", "S", "P"] * 10,
volume_per_atom=50)
map_target, tmp, tmp = compute_map(xray_structure=xrs)
xrs_sh = xrs.deep_copy_scatterers()
xrs_sh.shake_sites_in_place(mean_distance=0.8)
start_error = flex.mean(xrs.distances(other=xrs_sh))
print "Start:", start_error
map_current, miller_array, crystal_gridding = compute_map(
xray_structure=xrs_sh)
for step in [miller_array.d_min() / 4] * 5:
if (1):
minimized = real_space_target_and_gradients.minimization(
xray_structure=xrs_sh,
miller_array=miller_array,
crystal_gridding=crystal_gridding,
map_target=map_target,
max_iterations=500,
min_iterations=25,
step=step,
geometry_restraints_manager=None,
target_type="diff_map")
xrs_sh = minimized.xray_structure
map_current = minimized.map_current
final_error = flex.mean(
xrs.distances(other=minimized.xray_structure))
if (0):
minimized = real_space_refinement_simple.lbfgs(
sites_cart=xrs_sh.sites_cart(),
density_map=map_target,
unit_cell=xrs_sh.unit_cell(),
geometry_restraints_manager=None,
real_space_gradients_delta=step)
xrs_sh = xrs_sh.replace_sites_cart(minimized.sites_cart)
final_error = flex.mean(xrs.distances(other=xrs_sh))
print "Final:", final_error
assert approx_equal(start_error, 0.8, 1.e-3)
assert final_error < 1.e-4
print "OK"
def run():
def compute_map(xray_structure, d_min=1.5, resolution_factor=1./4):
fc = xray_structure.structure_factors(d_min = d_min).f_calc()
fft_map = fc.fft_map(resolution_factor=resolution_factor)
fft_map.apply_sigma_scaling()
result = fft_map.real_map_unpadded()
return result, fc, fft_map
xrs = random_structure.xray_structure(
space_group_info = sgtbx.space_group_info("P212121"),
elements = ["N","C","O","S","P"]*10,
volume_per_atom = 50)
map_target,tmp,tmp = compute_map(xray_structure = xrs)
xrs_sh = xrs.deep_copy_scatterers()
xrs_sh.shake_sites_in_place(mean_distance=0.8)
start_error = flex.mean(xrs.distances(other = xrs_sh))
print "Start:", start_error
map_current, miller_array, crystal_gridding = compute_map(
xray_structure = xrs_sh)
for step in [miller_array.d_min()/4]*5:
if(1):
minimized = real_space_target_and_gradients.minimization(
xray_structure = xrs_sh,
miller_array = miller_array,
crystal_gridding = crystal_gridding,
map_target = map_target,
max_iterations = 500,
min_iterations = 25,
step = step,
geometry_restraints_manager = None,
target_type = "diff_map")
xrs_sh = minimized.xray_structure
map_current = minimized.map_current
final_error = flex.mean(xrs.distances(other = minimized.xray_structure))
if(0):
minimized = real_space_refinement_simple.lbfgs(
sites_cart=xrs_sh.sites_cart(),
density_map=map_target,
unit_cell=xrs_sh.unit_cell(),
geometry_restraints_manager=None,
real_space_gradients_delta=step)
xrs_sh = xrs_sh.replace_sites_cart(minimized.sites_cart)
final_error = flex.mean(xrs.distances(other = xrs_sh))
print "Final:", final_error
assert approx_equal(start_error, 0.8, 1.e-3)
assert final_error < 1.e-4
print "OK"