def run(fmodel,
geometry_restraints_manager,
pdb_hierarchy,
solvent_selection,
optimize_hd = False,
log = None,
params = None):
if(log is None): log = sys.stdout
if(params is None): params = master_params().extract()
print_statistics.make_sub_header(text="Fitting sidechains", out=log)
mon_lib_srv = mmtbx.monomer_library.server.server()
if(params.use_dihedral_restraints):
sel = flex.bool(fmodel.xray_structure.scatterers().size(), True)
geometry_restraints_manager = geometry_restraints_manager.select(sel)
geometry_restraints_manager.remove_dihedrals_in_place(sel)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry_restraints_manager,
normalization = True)
model = mmtbx.model.manager(
restraints_manager = restraints_manager,
xray_structure = fmodel.xray_structure,
pdb_hierarchy = pdb_hierarchy)
backbone_selections = model.backbone_selections()
if(params.ignore_water_when_move_sidechains):
selection = ~model.solvent_selection()
else:
selection = flex.bool(model.xray_structure.scatterers().size(), True)
selection &= backbone_selections
fmt = "Macro-cycle %2d: r_work=%6.4f r_free=%6.4f"
print >> log, fmt%(0, fmodel.r_work(), fmodel.r_free())
for macro_cycle in range(1,params.number_of_macro_cycles+1):
target_map_data, fft_map_1 = get_map_data(fmodel = fmodel,
map_type = params.target_map,
exclude_free_r_reflections = params.exclude_free_r_reflections)
model_map_data,fft_map_2 = get_map_data(fmodel = fmodel,
map_type = params.model_map)
residual_map_data,fft_map_3 = get_map_data(fmodel = fmodel,
map_type = params.residual_map,
exclude_free_r_reflections = params.exclude_free_r_reflections)
if(params.filter_residual_map_value is not None): #XXX use filtering....
map_sel = flex.abs(residual_map_data) < params.filter_residual_map_value
residual_map_data = residual_map_data.set_selected(map_sel, 0)
if(params.filter_2fofc_map is not None):
map_sel = flex.abs(target_map_data) < params.filter_2fofc_map
target_map_data = target_map_data.set_selected(map_sel, 0)
rsr_manager = refiner(
pdb_hierarchy = pdb_hierarchy,
target_map = target_map_data,
geometry_restraints_manager = geometry_restraints_manager,
real_space_target_weight = params.residue_iteration.real_space_refine_target_weight,
real_space_gradients_delta = fmodel.f_obs().d_min()/4,
max_iterations = params.residue_iteration.real_space_refine_max_iterations)
residue_rsr_monitor = residue_iteration(
pdb_hierarchy = pdb_hierarchy,
xray_structure = fmodel.xray_structure,
selection = selection,
target_map_data = target_map_data,
model_map_data = model_map_data,
residual_map_data = residual_map_data,
mon_lib_srv = mon_lib_srv,
rsr_manager = rsr_manager,
optimize_hd = optimize_hd,
params = params.residue_iteration,
log = log)
fmodel.update_xray_structure(update_f_calc=True, update_f_mask=True)
print >> log, "1:", fmt%(macro_cycle, fmodel.r_work(), fmodel.r_free())
del target_map_data, model_map_data, residual_map_data, fft_map_1, fft_map_2, fft_map_3
if(params.validate_change):
validate_changes(fmodel = fmodel,
residue_rsr_monitor = residue_rsr_monitor,
validate_method=None,
log = log)
def run(fmodel,
geometry_restraints_manager,
pdb_hierarchy,
solvent_selection,
optimize_hd=False,
log=None,
params=None):
if (log is None): log = sys.stdout
if (params is None): params = master_params().extract()
print_statistics.make_sub_header(text="Fitting sidechains", out=log)
mon_lib_srv = mmtbx.monomer_library.server.server()
if (params.use_dihedral_restraints):
sel = flex.bool(fmodel.xray_structure.scatterers().size(), True)
geometry_restraints_manager = geometry_restraints_manager.select(sel)
geometry_restraints_manager.remove_dihedrals_in_place(sel)
restraints_manager = mmtbx.restraints.manager(
geometry=geometry_restraints_manager, normalization=True)
model = mmtbx.model.manager(restraints_manager=restraints_manager,
xray_structure=fmodel.xray_structure,
pdb_hierarchy=pdb_hierarchy)
backbone_selections = model.backbone_selections()
if (params.ignore_water_when_move_sidechains):
selection = ~model.solvent_selection()
else:
selection = flex.bool(model.xray_structure.scatterers().size(), True)
selection &= backbone_selections
fmt = "Macro-cycle %2d: r_work=%6.4f r_free=%6.4f"
print >> log, fmt % (0, fmodel.r_work(), fmodel.r_free())
for macro_cycle in range(1, params.number_of_macro_cycles + 1):
target_map_data, fft_map_1 = get_map_data(
fmodel=fmodel,
map_type=params.target_map,
exclude_free_r_reflections=params.exclude_free_r_reflections)
model_map_data, fft_map_2 = get_map_data(fmodel=fmodel,
map_type=params.model_map)
residual_map_data, fft_map_3 = get_map_data(
fmodel=fmodel,
map_type=params.residual_map,
exclude_free_r_reflections=params.exclude_free_r_reflections)
if (params.filter_residual_map_value
is not None): #XXX use filtering....
map_sel = flex.abs(
residual_map_data) < params.filter_residual_map_value
residual_map_data = residual_map_data.set_selected(map_sel, 0)
if (params.filter_2fofc_map is not None):
map_sel = flex.abs(target_map_data) < params.filter_2fofc_map
target_map_data = target_map_data.set_selected(map_sel, 0)
rsr_manager = refiner(
pdb_hierarchy=pdb_hierarchy,
target_map=target_map_data,
geometry_restraints_manager=geometry_restraints_manager,
real_space_target_weight=params.residue_iteration.
real_space_refine_target_weight,
real_space_gradients_delta=fmodel.f_obs().d_min() / 4,
max_iterations=params.residue_iteration.
real_space_refine_max_iterations)
residue_rsr_monitor = residue_iteration(
pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
selection=selection,
target_map_data=target_map_data,
model_map_data=model_map_data,
residual_map_data=residual_map_data,
mon_lib_srv=mon_lib_srv,
rsr_manager=rsr_manager,
optimize_hd=optimize_hd,
params=params.residue_iteration,
log=log)
fmodel.update_xray_structure(update_f_calc=True, update_f_mask=True)
print >> log, "1:", fmt % (macro_cycle, fmodel.r_work(),
fmodel.r_free())
del target_map_data, model_map_data, residual_map_data, fft_map_1, fft_map_2, fft_map_3
if (params.validate_change):
validate_changes(fmodel=fmodel,
residue_rsr_monitor=residue_rsr_monitor,
validate_method=None,
log=log)
def run(
fmodel,
geometry_restraints_manager,
pdb_hierarchy,
solvent_selection,
secondary_structure=None,
params=None,
optimize_hd=False,
log=None,
):
from mmtbx.refinement import print_statistics
from mmtbx.secondary_structure import proteins
import mmtbx.restraints
import mmtbx.model
from scitbx.array_family import flex
if log is None:
log = sys.stdout
if params is None:
params = master_params().extract()
if secondary_structure is None:
import mmtbx.secondary_structure
secondary_structure = mmtbx.secondary_structure.manager(pdb_hierarchy=pdb_hierarchy)
print_statistics.make_sub_header(text="Peptide bond flips", out=log)
validator = ramachandran_validator()
restraints_manager = mmtbx.restraints.manager(geometry=geometry_restraints_manager, normalization=True)
model = mmtbx.model.manager(
restraints_manager=restraints_manager, xray_structure=fmodel.xray_structure, pdb_hierarchy=pdb_hierarchy
)
backbone_selections = model.backbone_selections()
if params.ignore_water_when_flipping:
selection = ~model.solvent_selection()
else:
selection = flex.bool(model.xray_structure.scatterers().size(), True)
selection &= backbone_selections
fmt = "Macro-cycle %2d: r_work=%6.4f r_free=%6.4f"
print >> log, fmt % (0, fmodel.r_work(), fmodel.r_free())
n_mac = params.number_of_macro_cycles
if n_mac is None:
n_mac = 0
for macro_cycle in range(1, n_mac + 1):
target_map_data, fft_map_1 = fit_rotamers.get_map_data(fmodel=fmodel, map_type=params.target_map)
model_map_data, fft_map_2 = fit_rotamers.get_map_data(fmodel=fmodel, map_type=params.model_map)
residual_map_data, fft_map_3 = fit_rotamers.get_map_data(fmodel=fmodel, map_type=params.residual_map)
if params.filter_residual_map_value is not None: # XXX use filtering....
map_sel = flex.abs(residual_map_data) < params.filter_residual_map_value
residual_map_data = residual_map_data.set_selected(map_sel, 0)
if params.filter_2fofc_map is not None:
map_sel = flex.abs(target_map_data) < params.filter_2fofc_map
target_map_data = target_map_data.set_selected(map_sel, 0)
rsr_manager = fit_rotamers.refiner(
pdb_hierarchy=pdb_hierarchy,
target_map=target_map_data,
geometry_restraints_manager=geometry_restraints_manager,
real_space_target_weight=params.residue_iteration.real_space_refine_target_weight,
real_space_gradients_delta=fmodel.f_obs().d_min() / 4,
max_iterations=params.residue_iteration.real_space_refine_max_iterations,
)
secondary_structure.pdb_hierarchy = pdb_hierarchy
alpha_selection = secondary_structure.helix_selection(alpha_only=True)
if params.skip_approximate_helices:
cache = pdb_hierarchy.atom_selection_cache()
print >> log, "Looking for roughly helical residues. . ."
find_helices = proteins.find_helices_simple(pdb_hierarchy)
# find_helices.show(out=log)
print >> log, ""
ss_params = find_helices.as_restraint_groups()
if ss_params is not None:
for helix in ss_params.helix:
helix_selection = cache.selection(helix.selection)
alpha_selection |= helix_selection
residue_rsr_monitor = residue_iteration(
pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
selection=selection,
alpha_selection=alpha_selection,
target_map_data=target_map_data,
model_map_data=model_map_data,
residual_map_data=residual_map_data,
rsr_manager=rsr_manager,
params=params.residue_iteration,
validator=validator,
log=log,
)
fmodel.update_xray_structure(update_f_calc=True, update_f_mask=True)
print >> log, "1:", fmt % (macro_cycle, fmodel.r_work(), fmodel.r_free())
del target_map_data, model_map_data, residual_map_data, fft_map_1, fft_map_2, fft_map_3
if params.real_space_refine_overall:
pass
# FIXME this method has completely disappeared...
# fit_rotamers.rsr_overall(
# model=model,
# fmodel=fmodel,
# params=params,
# optimize_hd=optimize_hd,
# macro_cycle=macro_cycle,
# log=log)
# print >> log, "1:", fmt%(macro_cycle, fmodel.r_work(), fmodel.r_free())
if params.validate_change:
fit_rotamers.validate_changes(
fmodel=fmodel, residue_rsr_monitor=residue_rsr_monitor, validate_method=validator, log=log
)
pdb_hierarchy.atoms().set_xyz(fmodel.xray_structure.sites_cart())