def exercise():
"""
Exercise refine "easy" with DNA/RNA.
"""
pi_good = get_pdb_inputs(pdb_str=pdb_str_answer, restraints=False)
map_data = get_map(xrs=pi_good.xrs)
xrs_good = pi_good.xrs.deep_copy_scatterers()
pi_good.ph.write_pdb_file(file_name="answer.pdb",
crystal_symmetry=xrs_good.crystal_symmetry())
#
pi_poor = get_pdb_inputs(pdb_str=pdb_str_poor, restraints=True)
pi_poor.ph.write_pdb_file(file_name="poor.pdb")
xrs_poor = pi_poor.xrs.deep_copy_scatterers()
#
d = xrs_good.distances(other=xrs_poor)
print d.min_max_mean().as_tuple()
assert flex.max(d)>2
assert flex.mean(d)>0.7
#
xrs_refined = xrs_poor
for i in xrange(3):
ero = individual_sites.easy(
map_data = map_data,
xray_structure = xrs_refined,
pdb_hierarchy = pi_poor.ph,
geometry_restraints_manager = pi_poor.grm)
xrs_refined = ero.xray_structure
# comapre
d = xrs_good.distances(other=xrs_refined)
print d.min_max_mean().as_tuple()
assert flex.max(d)<0.15
assert flex.mean(d)<0.03
ero.pdb_hierarchy.write_pdb_file(file_name="refined.pdb",
crystal_symmetry=xrs_good.crystal_symmetry())
def exercise():
"""
Exercise refine "easy" with DNA/RNA.
"""
pi_good = get_pdb_inputs(pdb_str=pdb_str_answer, restraints=False)
map_data = get_map(xrs=pi_good.xrs)
xrs_good = pi_good.xrs.deep_copy_scatterers()
pi_good.ph.write_pdb_file(file_name="answer.pdb",
crystal_symmetry=xrs_good.crystal_symmetry())
#
pi_poor = get_pdb_inputs(pdb_str=pdb_str_poor, restraints=True)
pi_poor.ph.write_pdb_file(file_name="poor.pdb")
xrs_poor = pi_poor.xrs.deep_copy_scatterers()
#
d = xrs_good.distances(other=xrs_poor)
print d.min_max_mean().as_tuple()
assert flex.max(d) > 2
assert flex.mean(d) > 0.7
#
xrs_refined = xrs_poor
for i in xrange(3):
ero = individual_sites.easy(map_data=map_data,
xray_structure=xrs_refined,
pdb_hierarchy=pi_poor.ph,
geometry_restraints_manager=pi_poor.grm)
xrs_refined = ero.xray_structure
# comapre
d = xrs_good.distances(other=xrs_refined)
print d.min_max_mean().as_tuple()
assert flex.max(d) < 0.15
assert flex.mean(d) < 0.03
ero.pdb_hierarchy.write_pdb_file(
file_name="refined.pdb", crystal_symmetry=xrs_good.crystal_symmetry())
def flip_and_refine(pdb_hierarchy,
xray_structure,
target_map,
geometry_restraints_manager,
chain,
res_num,
alt_loc = None,
n_refine_cycles = 3,
log = sys.stdout):
sites_cart = xray_structure.sites_cart()
ero = False
for ch in pdb_hierarchy.chains():
if ch.id.strip() != chain : continue
for rg in ch.residue_groups():
if rg.resseq_as_int() != res_num : continue
if rg.have_conformers() and not alt_loc :
s = 'Specified residue has alternate conformations. Please specify '
raise RuntimeError(s + 'alt_loc on the command line')
for residue in rg.atom_groups():
if alt_loc and alt_loc != residue.altloc.strip():
continue
flip_base(residue, angle=180)
sites_cart.set_selected(residue.atoms().extract_i_seq(),
residue.atoms().extract_xyz())
xray_structure = xray_structure.replace_sites_cart(sites_cart)
sele = residue.atoms().extract_i_seq()
print >> log, 'real-space refinement BEGIN'.center(79,'*')
for i in range(n_refine_cycles):
print >> log, 'real-space refinement cycle %i...' % (i + 1)
ero = individual_sites.easy(
map_data = target_map,
xray_structure = xray_structure,
pdb_hierarchy = pdb_hierarchy,
geometry_restraints_manager = geometry_restraints_manager,
selection = sele)
print >> log, 'real-space refinement FINISHED'.center(79,'*')
if not ero : raise RuntimeError('Specified residue not found')
return ero.pdb_hierarchy
def flip_and_refine(pdb_hierarchy,
xray_structure,
target_map,
geometry_restraints_manager,
chain,
res_num,
alt_loc = None,
n_refine_cycles = 3,
log = sys.stdout) :
sites_cart = xray_structure.sites_cart()
ero = False
for ch in pdb_hierarchy.chains():
if ch.id.strip() != chain : continue
for rg in ch.residue_groups():
if rg.resseq_as_int() != res_num : continue
if rg.have_conformers() and not alt_loc :
s = 'Specified residue has alternate conformations. Please specify '
raise RuntimeError(s + 'alt_loc on the command line')
for residue in rg.atom_groups():
if alt_loc and alt_loc != residue.altloc.strip():
continue
flip_base(residue, angle=180)
sites_cart.set_selected(residue.atoms().extract_i_seq(),
residue.atoms().extract_xyz())
xray_structure = xray_structure.replace_sites_cart(sites_cart)
sele = residue.atoms().extract_i_seq()
print >> log, 'real-space refinement BEGIN'.center(79,'*')
for i in range(n_refine_cycles):
print >> log, 'real-space refinement cycle %i...' % (i + 1)
ero = individual_sites.easy(
map_data = target_map,
xray_structure = xray_structure,
pdb_hierarchy = pdb_hierarchy,
geometry_restraints_manager = geometry_restraints_manager,
selection = sele)
print >> log, 'real-space refinement FINISHED'.center(79,'*')
if not ero : raise RuntimeError('Specified residue not found')
return ero.pdb_hierarchy
def refine_rsr(self, pdb_obj, pdb_hier, pdb_xrs, map_data, restraints):
#restraints manager required, generated as part of structure data
#res_sigma is target for coordinate restraints
#refinement updates coordinates, so make a copy first
input_xrs = copy.deepcopy(pdb_xrs)
input_hier = copy.deepcopy(pdb_hier)
try:
#weight of 5.0 allows good movement into density
#speeds up by skipping weight calculation
ref_out = rsr.easy(map_data,
input_xrs,
input_hier,
restraints,
w=5.0,
max_iterations=100)
ref_xrs = ref_out.xray_structure
ref_hier = ref_out.pdb_hierarchy
except:
print "RSR of chainid,resid " + self.chainid + str(
self.resid) + " FAILED!"
#return unrefined structure (a bit dangerous)
ref_xrs = input_xrs
ref_hier = input_hier
return ref_xrs, ref_hier
def exercise():
"""
Exercise refine "easy" with DNA/RNA.
"""
pi_good = get_pdb_inputs(pdb_str=pdb_str_answer, restraints=False)
map_data = get_map(xrs=pi_good.xrs)
xrs_good = pi_good.xrs.deep_copy_scatterers()
pi_good.ph.write_pdb_file(file_name="answer.pdb",
crystal_symmetry=xrs_good.crystal_symmetry())
#
pi_poor = get_pdb_inputs(pdb_str=pdb_str_poor, restraints=True)
pi_poor.ph.write_pdb_file(file_name="poor.pdb")
xrs_poor = pi_poor.xrs.deep_copy_scatterers()
#
d = xrs_good.distances(other=xrs_poor)
print d.min_max_mean().as_tuple()
assert flex.max(d)>3
assert flex.mean(d)>1
chain = 'B'
res_num = 40
alt_loc = None
ero = False
n_refine_cycles = 3
target_map = get_map(xrs=pi_good.xrs)
sites_cart = xrs_poor.sites_cart()
for ch in pi_poor.ph.chains():
if ch.id.strip() != chain : continue
print 'chain'
for rg in ch.residue_groups():
if rg.resseq_as_int() != res_num : continue
print "res#"
if rg.have_conformers() and not alt_loc :
s = 'Specified residue has alternate conformations. Please specify '
raise RuntimeError(s + 'alt_loc on the command line')
for residue in rg.atom_groups():
if alt_loc and alt_loc != residue.altloc.strip():
continue
flipbase.flip_base(residue, angle=180)
sites_cart.set_selected(residue.atoms().extract_i_seq(),
residue.atoms().extract_xyz())
xray_structure = xrs_poor.replace_sites_cart(sites_cart)
sele = residue.atoms().extract_i_seq()
print 'real-space refinement BEGIN'.center(79,'*')
for i in range(n_refine_cycles):
print 'real-space refinement cycle %i...' % (i + 1)
ero = individual_sites.easy(
map_data = target_map,
xray_structure = xray_structure,
pdb_hierarchy = pi_poor.ph,
geometry_restraints_manager = pi_poor.grm,
selection = sele)
print 'real-space refinement FINISHED'.center(79,'*')
xrs_refined = ero.xray_structure
if not ero : raise RuntimeError('Specified residue not found')
d = xrs_good.distances(other=xrs_refined)
print d.min_max_mean().as_tuple()
assert flex.max(d)<0.07
assert flex.mean(d)<0.03
ero.pdb_hierarchy.write_pdb_file(file_name="refined.pdb",
crystal_symmetry=xrs_good.crystal_symmetry())
def exercise():
"""
Exercise refine "easy" with DNA/RNA.
"""
pi_good = get_pdb_inputs(pdb_str=pdb_str_answer, restraints=False)
map_data = get_map(xrs=pi_good.xrs)
xrs_good = pi_good.xrs.deep_copy_scatterers()
pi_good.ph.write_pdb_file(file_name="answer.pdb", crystal_symmetry=xrs_good.crystal_symmetry())
#
pi_poor = get_pdb_inputs(pdb_str=pdb_str_poor, restraints=True)
pi_poor.ph.write_pdb_file(file_name="poor.pdb")
xrs_poor = pi_poor.xrs.deep_copy_scatterers()
#
d = xrs_good.distances(other=xrs_poor)
print d.min_max_mean().as_tuple()
assert flex.max(d) > 3
assert flex.mean(d) > 1
chain = "B"
res_num = 40
alt_loc = None
ero = False
n_refine_cycles = 3
target_map = get_map(xrs=pi_good.xrs)
sites_cart = xrs_poor.sites_cart()
for ch in pi_poor.ph.chains():
if ch.id.strip() != chain:
continue
print "chain"
for rg in ch.residue_groups():
if rg.resseq_as_int() != res_num:
continue
print "res#"
if rg.have_conformers() and not alt_loc:
s = "Specified residue has alternate conformations. Please specify "
raise RuntimeError(s + "alt_loc on the command line")
for residue in rg.atom_groups():
if alt_loc and alt_loc != residue.altloc.strip():
continue
flipbase.flip_base(residue, angle=180)
sites_cart.set_selected(residue.atoms().extract_i_seq(), residue.atoms().extract_xyz())
xray_structure = xrs_poor.replace_sites_cart(sites_cart)
sele = residue.atoms().extract_i_seq()
print "real-space refinement BEGIN".center(79, "*")
for i in range(n_refine_cycles):
print "real-space refinement cycle %i..." % (i + 1)
ero = individual_sites.easy(
map_data=target_map,
xray_structure=xray_structure,
pdb_hierarchy=pi_poor.ph,
geometry_restraints_manager=pi_poor.grm,
selection=sele,
)
print "real-space refinement FINISHED".center(79, "*")
xrs_refined = ero.xray_structure
if not ero:
raise RuntimeError("Specified residue not found")
d = xrs_good.distances(other=xrs_refined)
print d.min_max_mean().as_tuple()
assert flex.max(d) < 0.07
assert flex.mean(d) < 0.03
ero.pdb_hierarchy.write_pdb_file(file_name="refined.pdb", crystal_symmetry=xrs_good.crystal_symmetry())