def exercise2():
pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 3988 P DA G 10 2.095 -23.407 14.671 1.00 24.76 P
ATOM 3989 OP1 DA G 10 2.702 -22.768 13.479 1.00 24.54 O
ATOM 3990 OP2 DA G 10 1.098 -22.688 15.497 1.00 26.02 O
ATOM 3991 O5' DA G 10 3.272 -23.890 15.629 1.00 22.57 O
ATOM 3992 C5' DA G 10 2.981 -24.494 16.871 1.00 21.71 C
ATOM 3993 C4' DA G 10 4.289 -24.903 17.501 1.00 21.29 C
ATOM 3994 O4' DA G 10 4.850 -25.979 16.721 1.00 20.23 O
ATOM 3995 C3' DA G 10 5.340 -23.803 17.483 1.00 20.46 C
ATOM 3996 O3' DA G 10 5.492 -23.313 18.807 1.00 20.49 O
ATOM 3997 C2' DA G 10 6.602 -24.471 16.925 1.00 18.76 C
ATOM 3998 C1' DA G 10 6.243 -25.951 16.910 1.00 17.49 C
ATOM 3999 N9 DA G 10 6.839 -26.749 15.842 1.00 14.88 N
ATOM 4000 C8 DA G 10 6.713 -26.565 14.492 1.00 15.01 C
ATOM 4001 N7 DA G 10 7.363 -27.452 13.774 1.00 15.05 N
ATOM 4002 C5 DA G 10 7.945 -28.283 14.718 1.00 13.74 C
ATOM 4003 C6 DA G 10 8.766 -29.426 14.610 1.00 12.94 C
ATOM 4004 N6 DA G 10 9.149 -29.944 13.443 1.00 13.28 N
ATOM 4005 N1 DA G 10 9.181 -30.024 15.746 1.00 12.16 N
ATOM 4006 C2 DA G 10 8.797 -29.503 16.921 1.00 14.06 C
ATOM 4007 N3 DA G 10 8.029 -28.435 17.152 1.00 13.57 N
ATOM 4008 C4 DA G 10 7.629 -27.865 15.998 1.00 13.67 C
""")
#open("tmp1.pdb", "w").write(pdb_in.hierarchy.as_pdb_string())
base = pdb_in.hierarchy.only_atom_group()
xyz = base.atoms().extract_xyz().deep_copy()
flipbase.flip_base(base, angle=180)
xyz_new = base.atoms().extract_xyz()
assert approx_equal(xyz_new.rms_difference(xyz), 2.45942)
def exercise2():
pdb_in = iotbx.pdb.hierarchy.input(
pdb_string="""\
ATOM 3988 P DA G 10 2.095 -23.407 14.671 1.00 24.76 P
ATOM 3989 OP1 DA G 10 2.702 -22.768 13.479 1.00 24.54 O
ATOM 3990 OP2 DA G 10 1.098 -22.688 15.497 1.00 26.02 O
ATOM 3991 O5' DA G 10 3.272 -23.890 15.629 1.00 22.57 O
ATOM 3992 C5' DA G 10 2.981 -24.494 16.871 1.00 21.71 C
ATOM 3993 C4' DA G 10 4.289 -24.903 17.501 1.00 21.29 C
ATOM 3994 O4' DA G 10 4.850 -25.979 16.721 1.00 20.23 O
ATOM 3995 C3' DA G 10 5.340 -23.803 17.483 1.00 20.46 C
ATOM 3996 O3' DA G 10 5.492 -23.313 18.807 1.00 20.49 O
ATOM 3997 C2' DA G 10 6.602 -24.471 16.925 1.00 18.76 C
ATOM 3998 C1' DA G 10 6.243 -25.951 16.910 1.00 17.49 C
ATOM 3999 N9 DA G 10 6.839 -26.749 15.842 1.00 14.88 N
ATOM 4000 C8 DA G 10 6.713 -26.565 14.492 1.00 15.01 C
ATOM 4001 N7 DA G 10 7.363 -27.452 13.774 1.00 15.05 N
ATOM 4002 C5 DA G 10 7.945 -28.283 14.718 1.00 13.74 C
ATOM 4003 C6 DA G 10 8.766 -29.426 14.610 1.00 12.94 C
ATOM 4004 N6 DA G 10 9.149 -29.944 13.443 1.00 13.28 N
ATOM 4005 N1 DA G 10 9.181 -30.024 15.746 1.00 12.16 N
ATOM 4006 C2 DA G 10 8.797 -29.503 16.921 1.00 14.06 C
ATOM 4007 N3 DA G 10 8.029 -28.435 17.152 1.00 13.57 N
ATOM 4008 C4 DA G 10 7.629 -27.865 15.998 1.00 13.67 C
"""
)
# open("tmp1.pdb", "w").write(pdb_in.hierarchy.as_pdb_string())
base = pdb_in.hierarchy.only_atom_group()
xyz = base.atoms().extract_xyz().deep_copy()
flipbase.flip_base(base, angle=180)
xyz_new = base.atoms().extract_xyz()
assert approx_equal(xyz_new.rms_difference(xyz), 2.45942)
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())