def tst_0():
model, map_data, crystal_symmetry = make_map_from_pdb(
raw_records=raw_records)
method = "rscc"
pdb_hierarchy_new = maptbx.loc_res(map=map_data,
model=model,
crystal_symmetry=crystal_symmetry,
chunk_size=10,
soft_mask_radius=3.,
method=method)
b_values, occs = get_b_and_occ(
hierarchy=pdb_hierarchy_new,
atom_selection="name CA and (resid 5 or resid 15)")
print("\nBvalues (resolutions): for %s: %s" % (method, str(b_values)))
assert approx_equal(b_values, [7.5, 3.0])
method = "fsc"
pdb_hierarchy_new = maptbx.loc_res(map=map_data,
model=model,
crystal_symmetry=crystal_symmetry,
chunk_size=10,
soft_mask_radius=3.,
method=method,
fsc_cutoff=0.143)
b_values, occs = get_b_and_occ(
hierarchy=pdb_hierarchy_new,
atom_selection="name CA and (resid 5 or resid 15)")
print("\nBvalues (resolutions): for %s: %s" % (method, str(b_values)))
assert approx_equal(b_values, [2.72, 2.27], eps=.05)
def tst_0():
ph,map_data,crystal_symmetry=make_map_from_pdb(raw_records=raw_records)
method="rscc"
pdb_hierarchy_new = maptbx.loc_res(
map = map_data,
pdb_hierarchy = ph,
crystal_symmetry = crystal_symmetry,
chunk_size = 10,
soft_mask_radius = 3.,
method = method)
b_values,occs=get_b_and_occ(hierarchy=pdb_hierarchy_new,
atom_selection="name CA and (resid 5 or resid 15)")
print "\nBvalues (resolutions): for %s: %s" %(method,str(b_values))
assert approx_equal(b_values,[5.8, 3.0])
method = "fsc"
pdb_hierarchy_new = maptbx.loc_res(
map = map_data,
pdb_hierarchy = ph,
crystal_symmetry = crystal_symmetry,
chunk_size = 10,
soft_mask_radius = 3.,
method = method,
fsc_cutoff = 0.143)
b_values,occs=get_b_and_occ(hierarchy=pdb_hierarchy_new,
atom_selection="name CA and (resid 5 or resid 15)")
print "\nBvalues (resolutions): for %s: %s" %(method,str(b_values))
assert approx_equal(b_values,[8.286411404892835, 2.1497394511476364],eps=.05)
def tst_1():
for set_b_iso, expected_b_values, expected_occs in zip(
[-200, 0, 200], [[200.0, 200.0], [-20.0, -20.0], [-160.0, -180.0]],
[[3.0, 3.0], [3.4, 3.0], [3.2, 3.1]]):
model, map_data, crystal_symmetry = make_map_from_pdb(
raw_records=raw_records_2, set_b_iso=set_b_iso)
method = "rscc_d_min_b"
print("Running test of rscc_d_min_b")
pdb_hierarchy_new = maptbx.loc_res(
map=map_data,
model=model,
crystal_symmetry=crystal_symmetry,
chunk_size=10,
method=method,
soft_mask_radius=3.,
hard_d_min=3.,
b_range_low=-1000,
b_range_high=1000,
)
b_values, occs = get_b_and_occ(
hierarchy=pdb_hierarchy_new,
atom_selection="name CA and (resid 5 or resid 15)")
print("Bvalues (b_sharpen) expected: %s found: %s " %
(str(expected_b_values), str(b_values)))
print("Occ values(d_min) expected: %s found: %s " %
(str(expected_occs), str(occs)))
assert approx_equal(expected_b_values, b_values)
assert approx_equal(expected_occs, occs)