def refit_residues(pdb_hierarchy,
cif_objects,
fmodel,
use_rotamers=True,
anneal=False,
verbose=True,
allow_modified_residues=False,
out=sys.stdout):
"""
Use real-space refinement tools to fit newly extended residues.
"""
from mmtbx.refinement.real_space import fit_residue
from mmtbx.rotamer import rotamer_eval
import mmtbx.monomer_library.server
from mmtbx import building
from scitbx.array_family import flex
mon_lib_srv = mmtbx.monomer_library.server.server()
rotamer_manager = rotamer_eval.RotamerEval()
ppdb_out = box_out = out
if (not verbose):
ppdb_out = null_out()
box_out = null_out()
make_sub_header("Processing new model", out=ppdb_out)
processed_pdb = building.reprocess_pdb(
pdb_hierarchy=pdb_hierarchy,
crystal_symmetry=fmodel.f_obs().crystal_symmetry(),
cif_objects=cif_objects,
out=ppdb_out)
print("", file=ppdb_out)
hierarchy = processed_pdb.all_chain_proxies.pdb_hierarchy
xrs = processed_pdb.xray_structure()
grm_geometry = processed_pdb.geometry_restraints_manager()
make_sub_header("Fitting residues", out=out)
target_map = fmodel.map_coefficients(
map_type="2mFo-DFc", exclude_free_r_reflections=True).fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map_unpadded()
unit_cell = xrs.unit_cell()
for chain in hierarchy.only_model().chains():
if (not chain.is_protein()) and (not allow_modified_residues): continue
residue_groups = chain.residue_groups()
for i_rg, residue_group in enumerate(residue_groups):
prev_res = next_res = None
atom_groups = residue_group.atom_groups()
if (len(atom_groups) > 1): continue
residue = atom_groups[0]
atoms = residue.atoms()
atoms.reset_tmp()
segids = atoms.extract_segid()
if (segids.all_eq("XXXX")):
sites_start = atoms.extract_xyz()
def get_two_fofc_mean(residue):
sum = 0
n_atoms = 0
for atom in residue.atoms():
if (not atom.element.strip() in ["H", "D"]):
site_frac = unit_cell.fractionalize(
site_cart=atom.xyz)
sum += target_map.eight_point_interpolation(
site_frac)
n_atoms += 1
assert (n_atoms > 0)
return sum / n_atoms
sites_start = atoms.extract_xyz().deep_copy()
two_fofc_mean_start = get_two_fofc_mean(residue)
refit = fit_residue.run_with_minimization(
target_map=target_map,
residue=residue,
xray_structure=xrs,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
geometry_restraints_manager=grm_geometry,
real_space_gradients_delta=fmodel.f_obs().d_min() * 0.25,
rms_bonds_limit=0.01,
rms_angles_limit=1.0,
backbone_sample_angle=20,
allow_modified_residues=allow_modified_residues)
two_fofc_mean_end = get_two_fofc_mean(residue)
sites_end = atoms.extract_xyz()
flag = ""
if (two_fofc_mean_end > two_fofc_mean_start):
flag = " <-- keep"
xrs = refit.xray_structure
else:
atoms.set_xyz(sites_start)
for atom in atoms:
atom.tmp = 1
print(" residue '%s' : rmsd=%5.3f 2fofc_start=%5.3f 2fofc_end=%5.3f%s" \
% (residue.id_str(), sites_end.rms_difference(sites_start),
two_fofc_mean_start, two_fofc_mean_end, flag), file=out)
return hierarchy, xrs
def real_space_refine (
pdb_hierarchy,
fmodel,
cif_objects,
params,
out,
nproc=None,
max_cycles=100, # arbitrarily large
remediate=False) :
from scitbx.array_family import flex
i_cycle = 0
while (i_cycle < max_cycles) :
print >> out, " Cycle %d:" % (i_cycle+1)
# this keeps track of which residues were split in the previous cycle -
# we only refine segments that have had residues added
rebuilt_flags = pdb_hierarchy.atoms().extract_tmp_as_size_t()
processed_pdb_file = building.reprocess_pdb(
pdb_hierarchy=pdb_hierarchy,
cif_objects=cif_objects,
crystal_symmetry=fmodel.xray_structure,
out=null_out())
# get the 2mFo-DFc map without new alternates!
#two_fofc_map = fmodel.two_fofc_map(exclude_free_r_reflections=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = pdb_hierarchy.atoms()
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints_manager = \
processed_pdb_file.geometry_restraints_manager(show_energies=False)
fmodel.update_xray_structure(xray_structure)
sele_cache = pdb_hierarchy.atom_selection_cache()
# FIXME very inefficient when looping!
# this will include both the newly built residues and the original atoms,
# including residues split to allow for backbone flexibility.
sele_split = sele_cache.selection(alt_confs.SELECTION_MODIFIED)
sele_main_conf = sele_cache.selection(alt_confs.SELECTION_OLD)
assert (len(sele_split) > 0)
k = 0
fragments = []
while (k < len(sele_split)) :
if (sele_split[k]) :
current_fragment = flex.size_t()
while (sele_split[k]) :
current_fragment.append(k)
k += 1
atom_start = pdb_atoms[current_fragment[0]].fetch_labels()
atom_end = pdb_atoms[current_fragment[-1]].fetch_labels()
frag_selection = flex.bool(sele_split.size(), current_fragment)
if (i_cycle > 0) :
flags = rebuilt_flags.select(frag_selection)
if flags.all_eq(0) :
continue
fragments.append(current_fragment)
else :
k += 1
if (len(fragments) == 0) :
pass
refine_fragments = rsr_fragments_parallel(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
processed_pdb_file=processed_pdb_file,
sele_main_conf=sele_main_conf,
rsr_fofc_map_target=(i_cycle==0 and params.cleanup.rsr_fofc_map_target))
refined = easy_mp.pool_map(
fixed_func=refine_fragments,
iterable=fragments,
processes=nproc)
sites_refined = pdb_atoms.extract_xyz()
for result in refined :
assert (result is not None)
result.show(out=out, prefix=" ")
sites_refined.set_selected(result.selection, result.sites_cart)
pdb_atoms.set_xyz(sites_refined)
xray_structure.set_sites_cart(sites_refined)
fmodel.update_xray_structure(xray_structure)
if (not remediate) or (max_cycles == 1) :
break
else :
for atom in pdb_hierarchy.atoms() :
if (atom.segid == alt_confs.SEGID_NEW_SPLIT) :
atom.segid = alt_confs.SEGID_NEW_REBUILT
print >> out, " checking for conformational strain..."
n_split = alt_confs.spread_alternates(
pdb_hierarchy=pdb_hierarchy,
new_occupancy=params.residue_fitting.expected_occupancy,
split_all_adjacent=False,
selection=alt_confs.SELECTION_NEW_REBUILT)
if (n_split > 0) :
print >> out, " split another %d residue(s) - will re-run RSR" % \
n_split
else :
break
i_cycle += 1
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=fmodel.xray_structure)
fmodel.update_xray_structure(xray_structure,
update_f_mask=True,
update_f_calc=True)
#fmodel.info().show_targets(out=out, text="After real-space refinement")
t2 = time.time()
return pdb_hierarchy
def real_space_refine(
pdb_hierarchy,
fmodel,
cif_objects,
params,
out,
nproc=None,
max_cycles=100, # arbitrarily large
remediate=False):
from scitbx.array_family import flex
i_cycle = 0
while (i_cycle < max_cycles):
print(" Cycle %d:" % (i_cycle + 1), file=out)
# this keeps track of which residues were split in the previous cycle -
# we only refine segments that have had residues added
rebuilt_flags = pdb_hierarchy.atoms().extract_tmp_as_size_t()
processed_pdb_file = building.reprocess_pdb(
pdb_hierarchy=pdb_hierarchy,
cif_objects=cif_objects,
crystal_symmetry=fmodel.xray_structure,
out=null_out())
# get the 2mFo-DFc map without new alternates!
#two_fofc_map = fmodel.two_fofc_map(exclude_free_r_reflections=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = pdb_hierarchy.atoms()
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints_manager = \
processed_pdb_file.geometry_restraints_manager(show_energies=False)
fmodel.update_xray_structure(xray_structure)
sele_cache = pdb_hierarchy.atom_selection_cache()
# FIXME very inefficient when looping!
# this will include both the newly built residues and the original atoms,
# including residues split to allow for backbone flexibility.
sele_split = sele_cache.selection(alt_confs.SELECTION_MODIFIED)
sele_main_conf = sele_cache.selection(alt_confs.SELECTION_OLD)
assert (len(sele_split) > 0)
k = 0
fragments = []
while (k < len(sele_split)):
if (sele_split[k]):
current_fragment = flex.size_t()
while (sele_split[k]):
current_fragment.append(k)
k += 1
atom_start = pdb_atoms[current_fragment[0]].fetch_labels()
atom_end = pdb_atoms[current_fragment[-1]].fetch_labels()
frag_selection = flex.bool(sele_split.size(), current_fragment)
if (i_cycle > 0):
flags = rebuilt_flags.select(frag_selection)
if flags.all_eq(0):
continue
fragments.append(current_fragment)
else:
k += 1
if (len(fragments) == 0):
pass
refine_fragments = rsr_fragments_parallel(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
processed_pdb_file=processed_pdb_file,
sele_main_conf=sele_main_conf,
rsr_fofc_map_target=(i_cycle == 0
and params.cleanup.rsr_fofc_map_target))
refined = easy_mp.pool_map(fixed_func=refine_fragments,
iterable=fragments,
processes=nproc)
sites_refined = pdb_atoms.extract_xyz()
for result in refined:
assert (result is not None)
result.show(out=out, prefix=" ")
sites_refined.set_selected(result.selection, result.sites_cart)
pdb_atoms.set_xyz(sites_refined)
xray_structure.set_sites_cart(sites_refined)
fmodel.update_xray_structure(xray_structure)
if (not remediate) or (max_cycles == 1):
break
else:
for atom in pdb_hierarchy.atoms():
if (atom.segid == alt_confs.SEGID_NEW_SPLIT):
atom.segid = alt_confs.SEGID_NEW_REBUILT
print(" checking for conformational strain...", file=out)
n_split = alt_confs.spread_alternates(
pdb_hierarchy=pdb_hierarchy,
new_occupancy=params.residue_fitting.expected_occupancy,
split_all_adjacent=False,
selection=alt_confs.SELECTION_NEW_REBUILT)
if (n_split > 0):
print(" split another %d residue(s) - will re-run RSR" % \
n_split, file=out)
else:
break
i_cycle += 1
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=fmodel.xray_structure)
fmodel.update_xray_structure(xray_structure,
update_f_mask=True,
update_f_calc=True)
#fmodel.info().show_targets(out=out, text="After real-space refinement")
t2 = time.time()
return pdb_hierarchy
def refit_residues (
pdb_hierarchy,
cif_objects,
fmodel,
use_rotamers=True,
anneal=False,
verbose=True,
allow_modified_residues=False,
out=sys.stdout) :
"""
Use real-space refinement tools to fit newly extended residues.
"""
from mmtbx.refinement.real_space import fit_residue
from mmtbx.rotamer import rotamer_eval
import mmtbx.monomer_library.server
from mmtbx import building
from scitbx.array_family import flex
mon_lib_srv = mmtbx.monomer_library.server.server()
rotamer_manager = rotamer_eval.RotamerEval()
ppdb_out = box_out = out
if (not verbose) :
ppdb_out = null_out()
box_out = null_out()
make_sub_header("Processing new model", out=ppdb_out)
processed_pdb = building.reprocess_pdb(
pdb_hierarchy=pdb_hierarchy,
crystal_symmetry=fmodel.f_obs().crystal_symmetry(),
cif_objects=cif_objects,
out=ppdb_out)
print >> ppdb_out, ""
hierarchy = processed_pdb.all_chain_proxies.pdb_hierarchy
xrs = processed_pdb.xray_structure()
grm_geometry = processed_pdb.geometry_restraints_manager()
make_sub_header("Fitting residues", out=out)
target_map = fmodel.map_coefficients(
map_type="2mFo-DFc",
exclude_free_r_reflections=True).fft_map(
resolution_factor=0.25).apply_sigma_scaling().real_map_unpadded()
unit_cell = xrs.unit_cell()
for chain in hierarchy.only_model().chains() :
if (not chain.is_protein()) and (not allow_modified_residues) : continue
residue_groups = chain.residue_groups()
for i_rg, residue_group in enumerate(residue_groups) :
prev_res = next_res = None
atom_groups = residue_group.atom_groups()
if (len(atom_groups) > 1) : continue
residue = atom_groups[0]
atoms = residue.atoms()
atoms.reset_tmp()
segids = atoms.extract_segid()
if (segids.all_eq("XXXX")) :
sites_start = atoms.extract_xyz()
def get_two_fofc_mean (residue) :
sum = 0
n_atoms = 0
for atom in residue.atoms() :
if (not atom.element.strip() in ["H","D"]) :
site_frac = unit_cell.fractionalize(site_cart=atom.xyz)
sum += target_map.eight_point_interpolation(site_frac)
n_atoms += 1
assert (n_atoms > 0)
return sum / n_atoms
sites_start = atoms.extract_xyz().deep_copy()
two_fofc_mean_start = get_two_fofc_mean(residue)
refit = fit_residue.run_with_minimization(
target_map=target_map,
residue=residue,
xray_structure=xrs,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
geometry_restraints_manager=grm_geometry,
real_space_gradients_delta=fmodel.f_obs().d_min()*0.25,
rms_bonds_limit=0.01,
rms_angles_limit=1.0,
backbone_sample_angle=20,
allow_modified_residues=allow_modified_residues)
two_fofc_mean_end = get_two_fofc_mean(residue)
sites_end = atoms.extract_xyz()
flag = ""
if (two_fofc_mean_end > two_fofc_mean_start) :
flag = " <-- keep"
xrs = refit.xray_structure
else :
atoms.set_xyz(sites_start)
for atom in atoms :
atom.tmp = 1
print >> out, \
" residue '%s' : rmsd=%5.3f 2fofc_start=%5.3f 2fofc_end=%5.3f%s" \
% (residue.id_str(), sites_end.rms_difference(sites_start),
two_fofc_mean_start, two_fofc_mean_end, flag)
return hierarchy, xrs
