def create_asu(ncs_filename,asu_filename,crystal_symmetry=None):
''' (str,str) -> crystal_symmetry object
Create ASU from NCS and save the new pdb file
with CRYST1 and SCALE records in local directory
Argument:
---------
ncs_filename : NCS to be used to create the ASU
asu_filename : ASU file name
crystal_symmetry : Allow forcing other crystal_symmetry
Returns:
--------
crystal_symmetry
'''
m = multimer(ncs_filename,'cau',error_handle=True,eps=1e-2)
if m.number_of_transforms == 0:
print 'Number of transforms is zero'
m.write(asu_filename)
pdb_inp = pdb.input(file_name = asu_filename)
xrs = pdb_inp.xray_structure_simple()
if not crystal_symmetry:
crystal_symmetry = xrs.crystal_symmetry()
pdb_inp.write_pdb_file(file_name = asu_filename, crystal_symmetry = crystal_symmetry)
return crystal_symmetry
def create_asu(self,ncs_filename,asu_filename,crystal_symmetry=None):
""" (str,str) -> crystal_symmetry object
Create P1 crystal_symmetry that fit the ASU.
Create ASU from NCS and save the new pdb file
with CRYST1 and SCALE records in local directory
Argument:
---------
ncs_filename : NCS to be used to create the ASU
asu_filename : ASU file name
crystal_symmetry : Allow forcing other crystal_symmetry
Returns:
--------
crystal_symmetry
"""
m = multimer(
file_name=ncs_filename,
reconstruction_type='cau',error_handle=True,eps=1e-2)
msg = 'Number of transforms is {0} instead of {1}'\
.format(m.number_of_transforms,2)
assert m.number_of_transforms == 2, msg
m.write(asu_filename)
pdb_inp = pdb.input(file_name = asu_filename)
xrs = pdb_inp.xray_structure_simple()
xrs_unit_cell = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=2)
if not crystal_symmetry:
crystal_symmetry = xrs_unit_cell.crystal_symmetry()
pdb_inp.write_pdb_file(file_name = asu_filename, crystal_symmetry = crystal_symmetry)
return crystal_symmetry
def test_BIOMT(self):
'''Test MTRIX record processing'''
# print sys._getframe().f_code.co_name
ba_expected_results = [
[1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0], [-1.0, 1.0, 1.0], [1.0, 1.0, -1.0],
[-1.0, 1.0, -1.0], [-0.366025, 1.366025, 1.0], [-1.366025, 0.366025, 1.0], [1.0, 1.5, 1.0],
[-1.366025, 0.366025, 0.0], [94.618, -5.253, 91.582], [94.618, -91.582, -5.253],
[91.582, -5.253, -94.618], [5.253, 94.618, 91.582], [91.582, -5.253, -94.618],
[5.253, 91.582, -94.618], [51.858229, 79.315053, 91.582], [-42.759771, 84.568053, 91.582],
[94.618, -4.753, 91.582], [-42.759771, 84.568053, 90.582], [62.395, 51.344, 80.786],
[62.395, -80.786, 51.344], [80.786, 51.344, -62.395], [-51.344, 62.395, 80.786],
[80.786, 51.344, -62.395], [-51.344, 80.786, -62.395], [-13.267688, 79.70763, 80.786],
[-75.662688, 28.36363, 80.786], [62.395, 51.844, 80.786], [-75.662688, 28.36363, 79.786],
[39.954, 51.526, 72.372], [39.954, -72.372, 51.526], [72.372, 51.526, -39.954],
[-51.526, 39.954, 72.372], [72.372, 51.526, -39.954], [-51.526, 72.372, -39.954],
[-24.645804, 60.364163, 72.372], [-64.599804, 8.838163, 72.372], [39.954, 52.026, 72.372],
[-64.599804, 8.838163, 71.372]]
# use BIOMT data
ba_multimer_data = multimer(
file_name='multimer_test_data.pdb',
reconstruction_type='ba')
ba_multimer_xyz = list(ba_multimer_data.sites_cart())
assert ba_multimer_data.new_annotation is None
# The multimer processing is my chain, so we need to sort lists before we compare them
ba_multimer_xyz.sort()
ba_expected_results.sort()
assert approx_equal(ba_expected_results,ba_multimer_xyz,eps=0.001)
self.assertEqual(ba_multimer_data.number_of_transforms,9)
def test_MTRIX(self):
'''Test MTRIX record processing'''
# print sys._getframe().f_code.co_name
cau_expected_results = [
[1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [-0.366025, 1.366025, 1.0], [-1.366025, 0.366025, 1.0],
[1.0, 1.5, 1.0], [94.618, -5.253, 91.582],
[94.618, -91.582, -5.253], [51.858229, 79.315053, 91.582], [-42.759771, 84.568053, 91.582],
[94.618, -4.753, 91.582], [62.395, 51.344, 80.786],
[62.395, -80.786, 51.344], [-13.267688, 79.70763, 80.786], [-75.662688, 28.36363, 80.786],
[62.395, 51.844, 80.786], [39.954, 51.526, 72.372],
[39.954, -72.372, 51.526], [-24.645804, 60.364163, 72.372], [-64.599804, 8.838163, 72.372],
[39.954, 52.026, 72.372]]
# use MTRIX data
multimer_data = multimer(
file_name='multimer_test_data.pdb',
reconstruction_type='cau')
cau_multimer_xyz = list(multimer_data.sites_cart())
cau_multimer_xyz.sort()
cau_expected_results.sort()
assert approx_equal(cau_expected_results,cau_multimer_xyz,eps=0.001)
# Test that the number of MTRIX record to process is correct
self.assertEqual(multimer_data.number_of_transforms,4)
# Test getting non-rounded ASU
source_xyz = multimer_data.get_ncs_hierarchy().atoms().extract_xyz()
xyz = apply_transforms(
ncs_coordinates = source_xyz,
ncs_restraints_group_list = multimer_data.get_ncs_restraints_group_list(),
total_asu_length = multimer_data.total_asu_length(),
extended_ncs_selection = flex.size_t_range(source_xyz.size()),
round_coordinates=False)
cau_multimer_xyz = list(xyz)
cau_multimer_xyz.sort()
assert approx_equal(cau_expected_results,cau_multimer_xyz,eps=0.00001)
# Test multimer without rounding
multimer_data = multimer(
file_name='multimer_test_data.pdb',
round_coordinates=False,
reconstruction_type='cau')
cau_multimer_xyz = list(multimer_data.sites_cart())
cau_multimer_xyz.sort()
cau_expected_results.sort()
assert approx_equal(cau_expected_results,cau_multimer_xyz,eps=0.00001)
def run():
# 1 NCS copy: starting template to generate whole asu; place into P1 box
pdb_inp = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
mtrix_object = pdb_inp.process_mtrix_records()
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
xrs_one_ncs = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
ph.adopt_xray_structure(xrs_one_ncs)
of = open("one_ncs_in_asu.pdb", "w")
print >> of, mtrix_object.format_MTRIX_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs_one_ncs.crystal_symmetry())
of.close()
# 1 NCS copy -> full asu (expand NCS). This is the answer-strucure
m = multimer("one_ncs_in_asu.pdb",'cau',error_handle=True,eps=1e-2)
assert m.number_of_transforms == 2, m.number_of_transforms
xrs_asu = m.assembled_multimer.extract_xray_structure(
crystal_symmetry = xrs_one_ncs.crystal_symmetry())
m.write("full_asu.pdb")
assert xrs_asu.crystal_symmetry().is_similar_symmetry(
xrs_one_ncs.crystal_symmetry())
# Generate Fobs from answer structure
f_obs = abs(xrs_asu.structure_factors(d_min=2, algorithm="direct").f_calc())
r_free_flags = f_obs.generate_r_free_flags()
mtz_dataset = f_obs.as_mtz_dataset(column_root_label="F-obs")
mtz_dataset.add_miller_array(
miller_array=r_free_flags,
column_root_label="R-free-flags")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name = "data.mtz")
# Shake structure - subject to refinement input
xrs_shaken = xrs_one_ncs.deep_copy_scatterers()
xrs_shaken.shake_sites_in_place(mean_distance=0.3)
ph.adopt_xray_structure(xrs_shaken)
of = open("one_ncs_in_asu_shaken.pdb", "w")
print >> of, mtrix_object.format_MTRIX_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs.crystal_symmetry())
of.close()
### Refinement
params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
params.algorithm = "direct"
fmodel = mmtbx.f_model.manager(
f_obs = f_obs,
r_free_flags = r_free_flags,
xray_structure = xrs_one_ncs,
sf_and_grads_accuracy_params = params,
target_name = "ls_wunit_k1")
print "start r_factor: %6.4f" % fmodel.r_work()
for macro_cycle in xrange(60):
# refine coordinates
if(1):
minimized = minimizer(fmodel = fmodel, sites = True)
print " macro_cycle %3d (sites) r_factor: %6.4f"%(macro_cycle,
fmodel.r_work())
# refine ADPs
if(0):
minimized = minimizer(fmodel = fmodel, u_iso = True)
print " macro_cycle %3d (adp) r_factor: %6.4f"%(macro_cycle,
fmodel.r_work())
def build_asu(self,file_name_ncs,file_name_asu):
"""Build ASU from NCS and save the new pdb file in local directory"""
m = multimer(
pdb_input_file_name=file_name_ncs,
reconstruction_type='cau',
error_handle=True,
eps=0.01)
m.write(pdb_output_file_name=file_name_asu)
return m
def run():
pdb_dir = os.environ["PDB_MIRROR_PDB"]
pdb_files = open(os.path.join(pdb_dir, "INDEX"), "r").readlines()
pdb_code_list = [
'3p0s', '2wws', '2xpj', '2bfu', '3n7x', '2iz9', '1dwn', '1ei7','2wzr',
'2vf1', '1m1c', '1llc', '1dzl', '2vf9', '3ntt', '4ar2','4gmp', '3vdd',
'3bcc', '3s4g', '3lob', '3qpr', '1tdi', '1ohg', '3e8k', '2qzv', '2e0z',
'1wcd', '4bcu', '1vcr', '1ng0', '3dar', '4f5x', '4g93', '1bcc', '2izw',
'1f2n', '1ny7', '3oah', '1vb4', '2gtl', '2g33', '2zzq', '2ws9', '1c8n',
'2w4z', '1x9t', '3r0r', '4gb3', '1vsz', '2g34', '2c4y', '1z7s', '1ddl',
'2bq5', '2c4z', '3fbm', '2gh8', '1qjx', '1f8v', '2iz8', '2bs1', '4aqq',
'1qju', '1x36', '1w39', '1x35', '1pgw', '2wff', '2vq0', '2fz2', '2fz1',
'1x9p', '3vbu', '3hag', '4gh4', '3chx', '1pgl', '1a37', '1lp3', '3zfe',
'4fts', '4fsj', '3raa', '2c4q', '1qjy', '4hl8', '3tn9', '3es5', '1js9',
'4gbt', '4fte', '2x5i', '2izn', '1zba', '1r2j', '1k5m', '2w4y', '2qqp',
'4jgy', '4ftb', '4ang', '3zfg', '3zff', '3cji', '2c51', '1vak', '1uf2',
'1ohf', '3ux1', '4g0r', '3s6p', '3ra4', '2bu1', '1laj', '1a34', '7msf',
'4iv1', '3ra9', '3ra8', '2xbo', '1h8t', '5msf', '4jgz', '3vbo', '2ztn',
'1b35', '6msf', '4aed', '3vbs', '3vbr', '3vbf', '3ra2', '3kz4', '1za7',
'1vb2', '1rhq', '4iv3', '3vbh', '3nou', '3not', '3nop', '2xgk', '2wbh',
'2qij', '2c50', '2buk', '1wce', '1tnv']
pdb_code_list = [
'3dar', '1vcr', '1r2j', '1a37', '1llc', '1tnv', '1tdi', '1w39', '1ny7',
'1ddl', '1c8n', '2bfu', '4gmp', '3vbr', '3vbu', '3vbo', '4jgy', '3es5',
'3nop', '3not', '3nou', '3bcc', '1bcc', '1z7s', '6msf', '2iz8', '7msf',
'2izn', '2c50', '2c51', '2iz9', '2c4y', '2c4z', '5msf', '2c4q', '2bu1',
'3raa', '3oah', '3ra2', '3ra9', '3ra8', '3ra4', '3qpr', '1ei7', '1a34',
'3chx', '2wbh', '2fz1', '2fz2', '2gh8', '1wcd', '3fbm', '4gb3', '1laj',
'3vbh', '1dzl', '3hag', '4iv3', '1js9', '3n7x', '4gh4', '4jgz', '3tn9',
'4iv1', '1vb2', '1vb4', '1vak', '3s4g', '2buk', '1x36', '4bcu', '1b35',
'2wzr', '1k5m', '2bq5', '1zba', '1pgw', '3vbs', '1x35', '3vbf', '1pgl',
'4fsj', '4fte', '4fts', '2e0z', '4ftb', '2w4y', '2w4z', '2qzv', '3vdd',
'3p0s', '1qjx', '1qjy', '1qju', '3r0r', '2bs1', '2ztn', '1x9t', '2zzq',
'1x9p', '4aqq', '1za7', '4ar2', '2wws', '2xpj', '4hl8', '3ntt', '2vf1',
'3ux1', '2xgk', '2izw', '3cji', '4gbt', '2vq0', '4g93', '2g34', '2qij',
'2g33', '1f2n', '4g0r', '1ng0', '2ws9', '2xbo', '2wff', '1wce', '1dwn',
'2vf9', '3zfe', '3zff', '3zfg', '2x5i', '1h8t', '3lob', '4ang', '2gtl',
'2qqp', '1f8v', '1m1c', '1lp3', '4aed', '3e8k', '1uf2', '1ohg', '1ohf',
'3s6p', '3kz4', '4f5x', '1vsz']
pdb_length = []
for fn in pdb_code_list:
file_path = [x.strip() for x in pdb_files if x[-12:-8]==fn][0]
print file_path
full_path = os.path.join(pdb_dir,file_path)
m = multimer(
file_name=full_path,
reconstruction_type='cau',
error_handle=True,eps=1e-2)
pdb_length.append([len(m.sites_cart()),fn])
pdb_length.sort()
print '='*60
print pdb_length[:5]
print '='*60
def get_pdb_file_info(self,pdb_id):
"""
Collect pdb file NCS and header info if there are NCS relations
and reslution >= 3
Args:
pdb_id (str): collect info for a single pdb file
Return:
new_rec (File_records object): object containing the collected info
"""
new_rec = File_records()
new_rec.pdb_id = pdb_id
fetched_file = pdb_id + '.pdb'
if not os.path.isfile(fetched_file):
fetched_file = fetch.get_pdb (
id=pdb_id, data_type='pdb',
mirror='rcsb',quiet=True,log=null_out())
else:
print 'file exist in local folder, did not fetch it..'
fn = os.path.realpath(fetched_file)
pdb_inp = iotbx.pdb.input(file_name=fn)
mtrix_info = pdb_inp.process_mtrix_records(eps=0.01)
t = (mtrix_info.as_pdb_string() == '')
t |= (not ncs_only(mtrix_info))
new_rec.only_master_in_pdb = not t
if len(mtrix_info.r) > 0 and new_rec.only_master_in_pdb:
m = multimer(file_name=fn,reconstruction_type='cau')
m.write(
pdb_output_file_name=fn,
crystal_symmetry=pdb_inp.crystal_symmetry())
# note that now the fn is a complete ASU
ncs_obj = iotbx.ncs.input(file_name=fn)
if (ncs_obj.number_of_ncs_groups == 0):
os.remove(fn)
return None
new_rec.n_ncs_groups = ncs_obj.number_of_ncs_groups
new_rec.n_ncs_copies = len(ncs_obj.ncs_transform)
pio = pdb_inp.get_r_rfree_sigma()
new_rec.resolution = pio.resolution
if new_rec.resolution and (new_rec.resolution < 3):
os.remove(fn)
return None
new_rec.year = pdb_inp.extract_header_year()
new_rec.experiment_type = pdb_inp.get_experiment_type()
new_rec.r_work_header = pio.r_work
new_rec.r_free_header = pio.r_free
try:
shutil.move(fn,self.asu_dir)
except:
# avoid error if file already exist
pass
return new_rec
def test_ignoring_mtrix_rec(self):
"""
Test ignoring MTRIX record when copies already present in file
"""
pdb_inp = pdb.input(source_info=None, lines=test_pdb_9)
m = multimer(
pdb_str=test_pdb_9,
round_coordinates=False,
reconstruction_type='cau',
error_handle=True,eps=1e-2)
n1 = m.assembled_multimer.atoms().size()
n2 = pdb_inp.atoms().size()
self.assertEqual(n1,n2)
def test_proper_biomat_application(self):
""" Test that when building bio-molecule and then finding NCS relatin
from it, we get the same rotation and translation"""
pdb_strings = [pdb_test_data7,pdb_test_data8]
methods = ['ba','cau']
for method,pdb_string in zip(methods,pdb_strings):
print "method:", method
pdb_inp = pdb.input(source_info=None, lines=pdb_string)
crystal_symmetry = pdb_inp.crystal_symmetry()
m = multimer(
pdb_str=pdb_string,
round_coordinates=False,
reconstruction_type=method,
error_handle=True,eps=1e-2)
# The exact transforms from pdb_string
r1_expected = matrix.sqr(
[0.309017, -0.951057, 0.0,0.951057, 0.309017,-0.0,0.0,0.0,1.0])
r2_expected = matrix.sqr(
[-0.809017,-0.587785,0.0,0.587785,-0.809017,-0.0,0.0,0.0,1.0])
t1_expected = matrix.col([0,0,7])
t2_expected = matrix.col([0,0,0])
# Look at biomt records retrieved from PDB file
if method == 'ba':
rec = pdb_inp.process_BIOMT_records()
else:
rec = pdb_inp.process_mtrix_records()
r1 = rec.r[1]
r2 = rec.r[2]
t1 = rec.t[1]
t2 = rec.t[2]
(the_same, transpose) = is_same_transform(r1,t1,r1_expected,t1_expected)
self.assertTrue(the_same)
(the_same, transpose)= is_same_transform(r2,t2,r2_expected,t2_expected)
self.assertTrue(the_same)
# Look at the rotation and translation found by the NCS search
s = m.assembled_multimer.as_pdb_string(crystal_symmetry=crystal_symmetry)
print "new h:", s
ncs_obj = ncs.input(pdb_string=s)
print "ncs_obj.number_of_ncs_groups", ncs_obj.number_of_ncs_groups
r1 = ncs_obj.ncs_transform['002'].r
t1 = ncs_obj.ncs_transform['002'].t
r2 = ncs_obj.ncs_transform['003'].r
t2 = ncs_obj.ncs_transform['003'].t
(the_same, transpose) = is_same_transform(r1,t1,r1_expected,t1_expected)
self.assertTrue(the_same)
(the_same, transpose)= is_same_transform(r2,t2,r2_expected,t2_expected)
self.assertTrue(the_same)
if method == 'ba':
self.assertEqual(ncs_obj.number_of_ncs_groups,1)
elif method == 'cau':
self.assertEqual(ncs_obj.number_of_ncs_groups,2)
def test_spec_file_format(self):
""" Verify that spec object are produced properly """
# print sys._getframe().f_code.co_name
multimer_data = multimer(
pdb_str=pdb_test_data2,
reconstruction_type='cau')
pdb_inp = pdb.input(source_info=None, lines=pdb_test_data2)
t_i = pdb_inp.process_mtrix_records()
pdb_h = pdb_inp.construct_hierarchy()
trans_obj = ncs.input(
hierarchy=pdb_h,
transform_info=t_i)
pdb_hierarchy_asu = multimer_data.assembled_multimer
# print "pdb_hierarchy_asu", pdb_hierarchy_asu.as_pdb_string()
spec_output = trans_obj.get_ncs_info_as_spec(
pdb_hierarchy_asu=pdb_hierarchy_asu)
trans_obj2 = ncs.input(spec_ncs_groups=spec_output)
# print "t1", trans_obj.ncs_transform
# print "t2", trans_obj2.ncs_transform
t1 = trans_obj.ncs_transform['0000000002'].r
t2 = trans_obj2.ncs_transform['0000000002'].r
self.assertEqual(t1,t2)
self.assertEqual(len(trans_obj.ncs_transform),len(trans_obj2.ncs_transform))
t1 = trans_obj.ncs_to_asu_selection
t1_expected = {'chain A or chain B':
['chain C or chain D', 'chain E or chain F']}
self.assertEqual(t1,t1_expected)
t2 = trans_obj2.ncs_to_asu_selection
t2_expected = {
'chain A and (resseq 1:3 or resseq 6:7)':
['chain C and (resseq 1:3 or resseq 6:7)',
'chain E and (resseq 1:3 or resseq 6:7)'],
'chain B and (resseq 4:5)':
['chain D and (resseq 4:5)', 'chain F and (resseq 4:5)']}
self.assertEqual(t2,t2_expected)
# print "trans_obj.tr_id_to_selection", trans_obj.tr_id_to_selection
t1 = trans_obj.tr_id_to_selection['chain A_0000000003']
t1_expected = ('chain A',
'chain E')
self.assertEqual(t1,t1_expected)
t2 = trans_obj2.tr_id_to_selection['chain A_0000000003']
t2_expected = ('chain A and (resseq 1:3 or resseq 6:7)',
'chain E and (resseq 1:3 or resseq 6:7)')
self.assertEqual(t2,t2_expected)
def biomt_reconstruction(args, command_name="phenix.pdb.biomt_reconstruction"):
''' (string) -> file
Reconstruction of the biological assembly multimer by applying
BIOMT transformation, from the REMARK 350 in the pdb file, to all
chains in file.
Produce a new pdb file containg the biological assembly multimer information
Arguments:
args: a string containing the pdb file name, 'file_name.pdb' and an
optional output file name. If no file name is given, the output
file will have the name 'biological_assembly_file_name.pdb'
>>> phenix.pdb.biomt_reconstruction input_file_name.pdb
bio-assembly reconstructed pdb file was added to your current directory
/path/biological_assembly_input_file_name.pdb
>>> phenix.pdb.biomt_reconstruction input_file_name.pdb output_file_name.pdb
bio-assembly reconstructed pdb file was added to your current directory
/path/output_file_name.pdb
@author: Youval Dar (LBL 2013)
'''
if (len(args) == 0):
raise Sorry('No input filename is given. Please provide a pdb file name. \n' + \
'>>> phenix.pdb.biomt_reconstruction input_file_name.pdb')
elif ('--help' in args) or ('-h' in args):
print help(biomt_reconstruction)
elif (len(args) > 2):
raise Sorry('To many input parameters are given')
elif not os.path.isfile(args[0]):
print 'There is no file {} in the current directory \n {}'.format(
args[0], os.getcwd())
raise Sorry('File name error')
else:
m = multimer(file_name=args[0], reconstruction_type='ba')
if m.number_of_transforms > 0:
# write the bio-assembly reconstructed file in current directory
if len(args) == 2:
# output file name given
m.write(args[1])
print '$s file was added to your current directory' % args[1]
else:
# output file name not given
m.write()
print 'bio-assembly reconstructed pdb file was added to your current directory'
print os.getcwd() + '/' + m.pdb_output_file_name
else:
print 'No BIOMT information in {}'.format(args[0])
def test_pdb_writing(self):
# print sys._getframe().f_code.co_name
"""
Verify that there are no errors processing the write command
No inception of the output is done.
To view the output change the write=False to ,write=True
"""
pdb_inp = pdb.input(source_info=None, lines=pdb_test_data2)
pdb_obj = pdb.hierarchy.input(pdb_string=pdb_test_data2)
transform_info = pdb_inp.process_mtrix_records()
transforms_obj = iotbx.ncs.input(
transform_info=transform_info,
hierarchy=pdb_inp.construct_hierarchy(),
exclude_selection=None)
multimer_data = multimer(
pdb_str=pdb_test_data2,
reconstruction_type='cau')
pdb_hierarchy_asu = multimer_data.assembled_multimer
# print '--- using ASU hierarchy ---'
pdbstr = transforms_obj.get_transform_records(
ncs_only=True,
pdb_hierarchy=pdb_hierarchy_asu,
write=False)
# print pdbstr
# print '='*50
pdbstr = transforms_obj.get_transform_records(
ncs_only=False,
pdb_hierarchy=pdb_hierarchy_asu,
write=False)
# print pdbstr
# print '--- using the hierarchy of only the master NCS ---'
pdbstr = transforms_obj.get_transform_records(
# pdb_hierarchy=pdb_obj.hierarchy,
pdb_hierarchy=pdb_hierarchy_asu,
biomt=True,
write=False)
# print pdbstr
# print '--- from xray structure ---'
xrs = pdb_hierarchy_asu.extract_xray_structure()
pdbstr = transforms_obj.get_transform_records(
# xrs=pdb_obj.xray_structure_simple(),
xrs=xrs,
biomt=True,
write=False)
def biomt_reconstruction(args, command_name="phenix.pdb.biomt_reconstruction"):
''' (string) -> file
Reconstruction of the biological assembly multimer by applying
BIOMT transformation, from the REMARK 350 in the pdb file, to all
chains in file.
Produce a new pdb file containg the biological assembly multimer information
Arguments:
args: a string containing the pdb file name, 'file_name.pdb' and an
optional output file name. If no file name is given, the output
file will have the name 'biological_assembly_file_name.pdb'
>>> phenix.pdb.biomt_reconstruction input_file_name.pdb
bio-assembly reconstructed pdb file was added to your current directory
/path/biological_assembly_input_file_name.pdb
>>> phenix.pdb.biomt_reconstruction input_file_name.pdb output_file_name.pdb
bio-assembly reconstructed pdb file was added to your current directory
/path/output_file_name.pdb
@author: Youval Dar (LBL 2013)
'''
if (len(args) == 0):
raise Sorry('No input filename is given. Please provide a pdb file name. \n' + \
'>>> phenix.pdb.biomt_reconstruction input_file_name.pdb')
elif ('--help' in args) or ('-h' in args):
print help(biomt_reconstruction)
elif (len(args) > 2):
raise Sorry('To many input parameters are given')
elif not os.path.isfile(args[0]):
print 'There is no file {} in the current directory \n {}'.format(args[0],os.getcwd())
raise Sorry('File name error')
else:
m = multimer(file_name=args[0],reconstruction_type='ba')
if m.number_of_transforms > 0:
# write the bio-assembly reconstructed file in current directory
if len(args) == 2:
# output file name given
m.write(args[1])
print '$s file was added to your current directory'%args[1]
else:
# output file name not given
m.write()
print 'bio-assembly reconstructed pdb file was added to your current directory'
print os.getcwd() + '/' + m.pdb_output_file_name
else:
print 'No BIOMT information in {}'.format(args[0])
def test_ignoring_mtrix_rec():
"""
Test raising Sorry for MTRIX record when copies already present in file
"""
pdb_inp = pdb.input(source_info=None, lines=test_pdb_9)
try:
m = multimer(
pdb_str=test_pdb_9,
round_coordinates=False,
reconstruction_type='cau',
error_handle=True,eps=1e-2)
except Exception as e:
assert e.message == "Copies are already present in the file"
else:
# There must be sorry.
assert 0
def mtrix_reconstruction(args, command_name="phenix.pdb.mtrix_reconstruction"):
''' (string) -> file
Reconstruction of the crystallographic asymmetric unit by applying
MTRIX transformation, from the MTRIX records in the pdb file, to all chains in file.
Produce a new pdb file containg the rystallographic asymmetric unit information
Arguments:
args: a string containing the pdb file name, 'file_name.pdb' and an optional output file name
if no file name is given, the output file will have the name 'cryst_asym_unit_file_name.pdb'
>>> phenix.pdb.mtrix_reconstruction input_file_name.pdb
mtrix-assembly reconstructed pdb file was added to your current directory
/path/cryst_asym_unit_input_file_name.pdb
>>> phenix.pdb.mtrix_reconstruction input_file_name.pdb 'output_file_name.pdb
mtrix-assembly reconstructed pdb file was added to your current directory
/path/output_file_name.pdb
@author: Youval Dar (LBL 2013)
'''
if (len(args) == 0):
raise Sorry('No input filename is given. Please provide a pdb file name. \n' + \
'>>> phenix.pdb.mtrix_reconstruction input_file_name.pdb')
elif ('--help' in args) or ('-h' in args):
print help(mtrix_reconstruction)
elif (len(args) > 2):
raise Sorry('To many input parameters are given')
elif not os.path.isfile(args[0]):
print 'There is no file {} in the current directory \n {}'.format(
args[0], os.getcwd())
raise Sorry('File name error')
else:
m = multimer(file_name=args[0], reconstruction_type='cau')
if m.number_of_transforms > 0:
# write the mtrix-assembly reconstructed file in current directory
if len(args) == 2:
# output file name given
m.write(args[1])
print '%s was added to your current directory' % args[1]
else:
# output file name not given
m.write()
print '%s was added to your current directory' % m.pdb_output_file_name
else:
print 'No MTRIX information in {}'.format(args[0])
def mtrix_reconstruction(args, command_name="phenix.pdb.mtrix_reconstruction"):
''' (string) -> file
Reconstruction of the crystallographic asymmetric unit by applying
MTRIX transformation, from the MTRIX records in the pdb file, to all chains in file.
Produce a new pdb file containg the rystallographic asymmetric unit information
Arguments:
args: a string containing the pdb file name, 'file_name.pdb' and an optional output file name
if no file name is given, the output file will have the name 'cryst_asym_unit_file_name.pdb'
>>> phenix.pdb.mtrix_reconstruction input_file_name.pdb
mtrix-assembly reconstructed pdb file was added to your current directory
/path/cryst_asym_unit_input_file_name.pdb
>>> phenix.pdb.mtrix_reconstruction input_file_name.pdb 'output_file_name.pdb
mtrix-assembly reconstructed pdb file was added to your current directory
/path/output_file_name.pdb
@author: Youval Dar (LBL 2013)
'''
if (len(args) == 0):
raise Sorry('No input filename is given. Please provide a pdb file name. \n' + \
'>>> phenix.pdb.mtrix_reconstruction input_file_name.pdb')
elif ('--help' in args) or ('-h' in args):
print help(mtrix_reconstruction)
elif (len(args) > 2):
raise Sorry('To many input parameters are given')
elif not os.path.isfile(args[0]):
print 'There is no file {} in the current directory \n {}'.format(args[0],os.getcwd())
raise Sorry('File name error')
else:
m = multimer(file_name=args[0],reconstruction_type='cau')
if m.number_of_transforms > 0:
# write the mtrix-assembly reconstructed file in current directory
if len(args) == 2:
# output file name given
m.write(args[1])
print '%s was added to your current directory'%args[1]
else:
# output file name not given
m.write()
print '%s was added to your current directory'%m.pdb_output_file_name
else:
print 'No MTRIX information in {}'.format(args[0])
def test_spec_file_format(self):
""" Verify that spec object are produced properly """
# print sys._getframe().f_code.co_name
multimer_data = multimer(
pdb_str=pdb_test_data2,
reconstruction_type='cau')
trans_obj = ncs.input(pdb_string=pdb_test_data2)
pdb_hierarchy_asu = multimer_data.assembled_multimer
spec_output = trans_obj.get_ncs_info_as_spec(
pdb_hierarchy_asu=pdb_hierarchy_asu,write=False)
trans_obj2 = ncs.input(spec_ncs_groups=spec_output)
t1 = trans_obj.ncs_transform['002'].r
t2 = trans_obj2.ncs_transform['002'].r
self.assertEqual(t1,t2)
self.assertEqual(len(trans_obj.ncs_transform),len(trans_obj2.ncs_transform))
t1 = trans_obj.ncs_to_asu_selection
t1_expected = {'chain A or chain B':
['chain E or chain F', 'chain C or chain D']}
self.assertEqual(t1,t1_expected)
t2 = trans_obj2.ncs_to_asu_selection
t2_expected = {
'chain A and (resseq 1:3 or resseq 6:7)':
['chain C and (resseq 1:3 or resseq 6:7)',
'chain E and (resseq 1:3 or resseq 6:7)'],
'chain B and (resseq 4:5)':
['chain D and (resseq 4:5)', 'chain F and (resseq 4:5)']}
self.assertEqual(t2,t2_expected)
t1 = trans_obj.tr_id_to_selection['chain A_003']
t1_expected = ('chain A',
'chain E')
self.assertEqual(t1,t1_expected)
t2 = trans_obj2.tr_id_to_selection['chain A_003']
t2_expected = ('chain A and (resseq 1:3 or resseq 6:7)',
'chain E and (resseq 1:3 or resseq 6:7)')
self.assertEqual(t2,t2_expected)
def test_writing_spec_file(self):
# print sys._getframe().f_code.co_name
"""
Verify that there are no errors processing the write command
No inception of the output is done. Just making sure it does not break
To view the output change the write=False to ,write=True
"""
transforms_obj = ncs_group_object()
pdb_inp = pdb.input(source_info=None, lines=pdb_test_data2)
pdb_obj = pdb.hierarchy.input(pdb_string=pdb_test_data2)
transform_info = pdb_inp.process_mtrix_records()
transforms_obj.preprocess_ncs_obj(
# transform_info=transform_info,
# pdb_hierarchy_inp=pdb_obj,
pdb_inp=pdb_inp)
asu = multimer(
pdb_str=pdb_test_data2,
reconstruction_type='cau')
transforms_obj.get_ncs_info_as_spec(
pdb_hierarchy_asu=asu.assembled_multimer,write=False)
def run(
n_macro_cycle=10,
sites=True,
u_iso=False,
run_finite_grad_differences_test = False):
"""
Arguments:
__________
n_macro_cycle : Number of refinement macro cycles
"""
# 1 NCS copy: starting template to generate whole asu; place into P1 box
pdb_inp = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
mtrix_object = pdb_inp.process_mtrix_records()
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
xrs_one_ncs = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
ph.adopt_xray_structure(xrs_one_ncs)
of = open("one_ncs_in_asu.pdb", "w")
print >> of, mtrix_object.format_MTRIX_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs_one_ncs.crystal_symmetry())
of.close()
# 1 NCS copy -> full asu (expand NCS). This is the answer-strucure
m = multimer("one_ncs_in_asu.pdb",'cau',error_handle=True,eps=1e-2)
assert m.number_of_transforms == 2, m.number_of_transforms
xrs_asu = m.assembled_multimer.extract_xray_structure(
crystal_symmetry = xrs_one_ncs.crystal_symmetry())
m.write("full_asu.pdb")
assert xrs_asu.crystal_symmetry().is_similar_symmetry(
xrs_one_ncs.crystal_symmetry())
# Generate Fobs from answer structure
f_obs = abs(xrs_asu.structure_factors(d_min=2, algorithm="direct").f_calc())
r_free_flags = f_obs.generate_r_free_flags()
mtz_dataset = f_obs.as_mtz_dataset(column_root_label="F-obs")
mtz_dataset.add_miller_array(
miller_array=r_free_flags,
column_root_label="R-free-flags")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name = "data.mtz")
# Shake structure - subject to refinement input
xrs_shaken = xrs_one_ncs.deep_copy_scatterers()
if sites:
xrs_shaken.shake_sites_in_place(mean_distance=0.3)
if u_iso:
xrs_shaken.shake_adp()
ph.adopt_xray_structure(xrs_shaken)
of = open("one_ncs_in_asu_shaken.pdb", "w")
print >> of, mtrix_object.format_MTRIX_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs.crystal_symmetry())
of.close()
### Refinement
params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
params.algorithm = "direct"
# Get the xray_structure of the shaken ASU
m_shaken = multimer(
pdb_input_file_name="one_ncs_in_asu_shaken.pdb",
reconstruction_type='cau',error_handle=True,eps=1e-2)
xrs_shaken_asu = m_shaken.assembled_multimer.as_pdb_input().\
xray_structure_simple(crystal_symmetry=xrs_one_ncs.crystal_symmetry())
# Save the shaken ASU for inspection
m_shaken.write(pdb_output_file_name='asu_shaken.pdb')
# Create a boolean selection string for selecting chains in NCS
selection_str = 'chain A'
ncs_selection = m_shaken.assembled_multimer.\
atom_selection_cache().selection(selection_str)
fmodel = mmtbx.f_model.manager(
f_obs = f_obs,
r_free_flags = r_free_flags,
xray_structure = xrs_shaken_asu,
sf_and_grads_accuracy_params = params,
target_name = "ls_wunit_k1")
print "start r_factor: %6.4f" % fmodel.r_work()
refine_method = 'sites'
for macro_cycle in xrange(n_macro_cycle):
# refine coordinates
if(sites):
minimized = minimizer(
fmodel = fmodel,
ncs_transformations_object=m,
ncs_atom_selection = ncs_selection,
run_finite_grad_differences_test = run_finite_grad_differences_test,
sites = True)
print " macro_cycle %3d (sites) r_factor: %6.4f"%(macro_cycle,
fmodel.r_work())
# refine ADPs
if(u_iso):
minimized = minimizer(
fmodel = fmodel,
ncs_transformations_object=m,
ncs_atom_selection = ncs_selection,
run_finite_grad_differences_test = run_finite_grad_differences_test,
u_iso = True)
print " macro_cycle %3d (adp) r_factor: %6.4f"%(macro_cycle,
fmodel.r_work())
if (0): save_pdb_file(
macro_cycle=macro_cycle,
fmodel=fmodel,
m_shaken=m_shaken,
u_iso=u_iso,
sites=sites)
if (1): save_pdb_file(
macro_cycle=macro_cycle,
fmodel=fmodel,
m_shaken=m_shaken,
u_iso=u_iso,
sites=sites)
def run_test(self):
# Refinement
params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
params.algorithm = "direct"
# Get the xray_structure of the shaken ASU
m_shaken = multimer(
file_name="one_ncs_in_asu_shaken.pdb",
round_coordinates=False,
reconstruction_type='cau',error_handle=True,eps=1e-2)
xrs_shaken_asu = m_shaken.assembled_multimer.extract_xray_structure(
crystal_symmetry=self.xrs_one_ncs.crystal_symmetry())
# force non-rounded coordinates into xray structure
xrs_shaken_asu.set_sites_cart(m_shaken.sites_cart())
# Save the shaken ASU for inspection
m_shaken.write(
pdb_output_file_name='asu_shaken.pdb',
crystal_symmetry=self.xrs_one_ncs.crystal_symmetry())
tr_obj = m_shaken.transforms_obj
self.ncs_restraints_group_list = tr_obj.get_ncs_restraints_group_list()
# refine both ncs related and not related atoms
self.refine_selection = flex.size_t(range(tr_obj.total_asu_length))
self.extended_ncs_selection = nu.get_extended_ncs_selection(
ncs_restraints_group_list=tr_obj.get_ncs_restraints_group_list(),
refine_selection=self.refine_selection)
assert self.refine_selection.size() == 21
self.fmodel = mmtbx.f_model.manager(
f_obs = self.f_obs,
r_free_flags = self.r_free_flags,
xray_structure = xrs_shaken_asu,
sf_and_grads_accuracy_params = params,
target_name = "ls_wunit_k1")
r_start = self.fmodel.r_work()
assert r_start > 0.1, r_start
print "start r_factor: %6.4f" % r_start
for macro_cycle in xrange(self.n_macro_cycle):
if self.transformations and \
not self.ncs_restraints_group_list: continue
data_weight = None
if(self.use_geometry_restraints):
data_weight = nu.get_weight(minimized_obj=self)
target_and_grads_object = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_reciprocal_space(
fmodel = self.fmodel,
ncs_restraints_group_list = self.ncs_restraints_group_list,
refine_selection = self.refine_selection,
restraints_manager = self.grm,
data_weight = data_weight,
refine_sites = self.sites,
refine_u_iso = self.u_iso,
refine_transformations = self.transformations,
iso_restraints = self.iso_restraints)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = target_and_grads_object,
xray_structure = self.fmodel.xray_structure,
ncs_restraints_group_list = self.ncs_restraints_group_list,
refine_selection = self.refine_selection,
finite_grad_differences_test = self.finite_grad_differences_test,
max_iterations = 100,
refine_sites = self.sites,
refine_u_iso = self.u_iso,
refine_transformations = self.transformations)
refine_type = 'adp'*self.u_iso + 'sites'*self.sites \
+ 'transformation'*self.transformations
outstr = " macro_cycle {0:3} ({1}) r_factor: {2:6.4f} " + \
self.finite_grad_differences_test * \
"finite_grad_difference_val: {3:.4f}"
print outstr.format(
macro_cycle, refine_type,self.fmodel.r_work(),
minimized.finite_grad_difference_val)
assert (minimized.finite_grad_difference_val < 1.0e-3)
assert approx_equal(self.fmodel.r_work(), target_and_grads_object.fmodel.r_work())
# break test if r_work is very small
if target_and_grads_object.fmodel.r_work() < 1.0e-6: break
# check results
if(self.u_iso):
assert approx_equal(self.fmodel.r_work(), 0, 1.e-5)
elif(self.sites):
if(self.use_geometry_restraints):
assert approx_equal(self.fmodel.r_work(), 0, 0.00015)
else:
assert approx_equal(self.fmodel.r_work(), 0, 1.e-5)
elif self.transformations:
assert approx_equal(self.fmodel.r_work(), 0, 0.0001)
else: assert 0
# output refined model
xrs_refined = self.fmodel.xray_structure
m_shaken.assembled_multimer.adopt_xray_structure(self.fmodel.xray_structure)
output_file_name = "refined_u_iso%s_sites%s.pdb"%(str(self.u_iso),
str(self.sites))
m_shaken.write(output_file_name)
self.test_files_names.append(output_file_name)
# check final model
if(not self.use_geometry_restraints):
# XXX fix later for case self.use_geometry_restraints=True
pdb_inp_answer = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
pdb_inp_refined = iotbx.pdb.input(file_name=output_file_name)
xrs1 = pdb_inp_answer.xray_structure_simple()
xrs2 = pdb_inp_refined.xray_structure_simple().select(
minimized.extended_ncs_selection)
mmtbx.utils.assert_xray_structures_equal(
x1 = xrs1,
x2 = xrs2,
sites = False)
delta = flex.vec3_double([xrs1.center_of_mass()]*xrs2.scatterers().size())-\
flex.vec3_double([xrs2.center_of_mass()]*xrs2.scatterers().size())
xrs2.set_sites_cart(sites_cart = xrs2.sites_cart()+delta)
mmtbx.utils.assert_xray_structures_equal(
x1 = xrs1,
x2 = xrs2)
def exercise_ss_multiplication():
pdb_str = """\
REMARK 350 BIOMT1 1 1.000000 -0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 -0.000000 1.000000 -0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 -0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 -0.809017 -0.500000 0.309017 0.00000
REMARK 350 BIOMT2 2 -0.500000 0.309017 -0.809017 0.00000
REMARK 350 BIOMT3 2 0.309017 -0.809017 -0.500000 0.00000
REMARK 350 BIOMT1 3 -0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 3 -0.000000 -0.000000 -1.000000 0.00000
REMARK 350 BIOMT3 3 -1.000000 0.000000 -0.000000 0.00000
REMARK 350 BIOMT1 4 0.809017 -0.500000 -0.309017 0.00000
REMARK 350 BIOMT2 4 -0.500000 -0.309017 -0.809017 0.00000
REMARK 350 BIOMT3 4 0.309017 0.809017 -0.500000 -0.00000
REMARK 350 BIOMT1 5 0.500000 0.309017 -0.809017 0.00000
REMARK 350 BIOMT2 5 -0.309017 -0.809017 -0.500000 0.00000
REMARK 350 BIOMT3 5 -0.809017 0.500000 -0.309017 0.00000
REMARK 350 BIOMT1 6 -0.309017 -0.809017 -0.500000 0.00000
REMARK 350 BIOMT2 6 -0.809017 0.500000 -0.309017 0.00000
REMARK 350 BIOMT3 6 0.500000 0.309017 -0.809017 -0.00000
REMARK 350 BIOMT1 7 -0.809017 0.500000 -0.309017 0.00000
REMARK 350 BIOMT2 7 0.500000 0.309017 -0.809017 0.00000
REMARK 350 BIOMT3 7 -0.309017 -0.809017 -0.500000 0.00000
REMARK 350 BIOMT1 8 -0.809017 -0.500000 -0.309017 0.00000
REMARK 350 BIOMT2 8 0.500000 -0.309017 -0.809017 0.00000
REMARK 350 BIOMT3 8 0.309017 -0.809017 0.500000 0.00000
REMARK 350 BIOMT1 9 -0.309017 0.809017 -0.500000 0.00000
REMARK 350 BIOMT2 9 -0.809017 -0.500000 -0.309017 0.00000
REMARK 350 BIOMT3 9 -0.500000 0.309017 0.809017 0.00000
HELIX 1 1 PRO A 28 LEU A 33 1 6
HELIX 7 7 ASP B 74 ALA B 79 1 6
HELIX 12 12 LYS C 151 TYR C 159 1 9
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 62 N PRO A 28 33.884 22.417 110.984 14.01 14.01 N
ATOM 63 CA PRO A 28 34.083 23.080 112.268 12.01 12.01 C
ATOM 64 C PRO A 28 32.908 24.004 112.604 12.01 12.01 C
ATOM 65 O PRO A 28 32.254 24.556 111.723 16.00 16.00 O
ATOM 66 CB PRO A 28 35.381 23.873 112.096 12.01 12.01 C
ATOM 67 CG PRO A 28 35.369 24.249 110.611 12.01 12.01 C
ATOM 68 CD PRO A 28 34.692 23.045 109.949 12.01 12.01 C
ATOM 69 N ASN A 29 32.694 24.235 113.899 14.01 14.01 N
ATOM 70 CA ASN A 29 31.700 25.147 114.485 12.01 12.01 C
ATOM 71 C ASN A 29 30.215 24.812 114.276 12.01 12.01 C
ATOM 72 O ASN A 29 29.406 25.211 115.111 16.00 16.00 O
ATOM 73 CB ASN A 29 32.013 26.616 114.122 12.01 12.01 C
ATOM 74 CG ASN A 29 33.381 27.082 114.575 12.01 12.01 C
ATOM 75 OD1 ASN A 29 34.061 26.468 115.379 16.00 16.00 O
ATOM 76 ND2 ASN A 29 33.841 28.204 114.073 14.01 14.01 N
ATOM 77 N GLU A 30 30.550 21.845 114.346 14.01 14.01 N
ATOM 78 CA GLU A 30 29.386 21.544 115.199 12.01 12.01 C
ATOM 79 C GLU A 30 29.802 20.720 116.428 12.01 12.01 C
ATOM 80 O GLU A 30 29.237 19.675 116.751 16.00 16.00 O
ATOM 81 CB GLU A 30 28.306 20.825 114.365 12.01 12.01 C
ATOM 82 CG GLU A 30 27.795 21.680 113.200 12.01 12.01 C
ATOM 83 CD GLU A 30 26.582 21.020 112.532 12.01 12.01 C
ATOM 84 OE1 GLU A 30 26.801 20.115 111.689 16.00 16.00 O
ATOM 85 OE2 GLU A 30 25.450 21.412 112.878 16.00 16.00 O
ATOM 86 N LEU A 31 29.828 23.005 116.792 14.01 14.01 N
ATOM 87 CA LEU A 31 29.299 22.073 115.816 12.01 12.01 C
ATOM 88 C LEU A 31 28.149 21.279 116.426 12.01 12.01 C
ATOM 89 O LEU A 31 28.305 20.133 116.853 16.00 16.00 O
ATOM 90 CB LEU A 31 30.413 21.167 115.268 12.01 12.01 C
ATOM 91 CG LEU A 31 31.519 21.894 114.483 12.01 12.01 C
ATOM 92 CD1 LEU A 31 32.517 20.866 113.958 12.01 12.01 C
ATOM 93 CD2 LEU A 31 30.995 22.696 113.286 12.01 12.01 C
ATOM 94 N GLY A 32 26.947 21.837 116.303 14.01 14.01 N
ATOM 95 CA GLY A 32 25.679 21.115 116.378 12.01 12.01 C
ATOM 96 C GLY A 32 25.506 20.004 115.323 12.01 12.01 C
ATOM 97 O GLY A 32 24.382 19.638 114.991 16.00 16.00 O
ATOM 98 N LEU A 33 26.624 19.470 114.815 14.01 14.01 N
ATOM 99 CA LEU A 33 26.791 18.378 113.866 12.01 12.01 C
ATOM 100 C LEU A 33 27.494 17.166 114.509 12.01 12.01 C
ATOM 101 O LEU A 33 27.549 16.110 113.890 16.00 16.00 O
ATOM 102 CB LEU A 33 27.595 18.877 112.644 12.01 12.01 C
ATOM 103 CG LEU A 33 27.192 20.239 112.037 12.01 12.01 C
ATOM 104 CD1 LEU A 33 28.098 20.578 110.853 12.01 12.01 C
ATOM 105 CD2 LEU A 33 25.745 20.281 111.549 12.01 12.01 C
ATOM 2090 N ASP B 74 21.209 34.482 113.075 14.01 14.01 N
ATOM 2091 CA ASP B 74 20.506 33.939 114.233 12.01 12.01 C
ATOM 2092 C ASP B 74 21.375 33.841 115.474 12.01 12.01 C
ATOM 2093 O ASP B 74 22.182 32.923 115.611 16.00 16.00 O
ATOM 2094 CB ASP B 74 19.906 32.571 113.907 12.01 12.01 C
ATOM 2095 CG ASP B 74 18.979 32.068 114.997 12.01 12.01 C
ATOM 2096 OD1 ASP B 74 19.110 32.533 116.149 16.00 16.00 O
ATOM 2097 OD2 ASP B 74 18.121 31.208 114.708 16.00 16.00 O
ATOM 2098 N MET B 75 21.194 34.811 116.364 14.01 14.01 N
ATOM 2099 CA MET B 75 21.934 34.884 117.610 12.01 12.01 C
ATOM 2100 C MET B 75 22.089 33.512 118.239 12.01 12.01 C
ATOM 2101 O MET B 75 23.123 33.213 118.837 16.00 16.00 O
ATOM 2102 CB MET B 75 21.234 35.824 118.583 12.01 12.01 C
ATOM 2103 CG MET B 75 21.525 37.288 118.322 12.01 12.01 C
ATOM 2104 SD MET B 75 23.242 37.703 118.659 32.07 32.07 S
ATOM 2105 CE MET B 75 23.058 38.659 120.162 12.01 12.01 C
ATOM 2106 N ILE B 76 21.067 32.672 118.091 14.01 14.01 N
ATOM 2107 CA ILE B 76 21.116 31.324 118.645 12.01 12.01 C
ATOM 2108 C ILE B 76 22.422 30.683 118.212 12.01 12.01 C
ATOM 2109 O ILE B 76 22.994 29.858 118.922 16.00 16.00 O
ATOM 2110 CB ILE B 76 19.929 30.457 118.191 12.01 12.01 C
ATOM 2111 CG1 ILE B 76 20.068 30.070 116.720 12.01 12.01 C
ATOM 2112 CG2 ILE B 76 18.618 31.182 118.436 12.01 12.01 C
ATOM 2113 CD1 ILE B 76 18.979 29.144 116.230 12.01 12.01 C
ATOM 2114 N LYS B 77 22.902 31.098 117.044 14.01 14.01 N
ATOM 2115 CA LYS B 77 24.160 30.591 116.525 12.01 12.01 C
ATOM 2116 C LYS B 77 25.209 30.734 117.613 12.01 12.01 C
ATOM 2117 O LYS B 77 26.219 30.038 117.612 16.00 16.00 O
ATOM 2118 CB LYS B 77 24.577 31.362 115.281 12.01 12.01 C
ATOM 2119 CG LYS B 77 23.624 31.194 114.112 12.01 12.01 C
ATOM 2120 CD LYS B 77 24.208 30.282 113.048 12.01 12.01 C
ATOM 2121 CE LYS B 77 25.656 30.627 112.741 12.01 12.01 C
ATOM 2122 NZ LYS B 77 25.986 32.047 113.045 14.01 14.01 N
ATOM 2123 N ILE B 78 24.954 31.644 118.547 14.01 14.01 N
ATOM 2124 CA ILE B 78 25.852 31.863 119.664 12.01 12.01 C
ATOM 2125 C ILE B 78 25.432 30.891 120.752 12.01 12.01 C
ATOM 2126 O ILE B 78 26.264 30.367 121.489 16.00 16.00 O
ATOM 2127 CB ILE B 78 25.788 33.314 120.171 12.01 12.01 C
ATOM 2128 CG1 ILE B 78 26.541 34.227 119.215 12.01 12.01 C
ATOM 2129 CG2 ILE B 78 26.405 33.447 121.552 12.01 12.01 C
ATOM 2130 CD1 ILE B 78 27.879 33.670 118.785 12.01 12.01 C
ATOM 2131 N ALA B 79 24.131 30.644 120.844 14.01 14.01 N
ATOM 2132 CA ALA B 79 23.615 29.721 121.839 12.01 12.01 C
ATOM 2133 C ALA B 79 24.401 28.426 121.758 12.01 12.01 C
ATOM 2134 O ALA B 79 25.260 28.159 122.591 16.00 16.00 O
ATOM 2135 CB ALA B 79 22.140 29.461 121.605 12.01 12.01 C
ATOM 4569 N LYS C 151 65.128 35.635 115.156 14.01 14.01 N
ATOM 4570 CA LYS C 151 65.530 35.389 113.777 12.01 12.01 C
ATOM 4571 C LYS C 151 64.991 36.467 112.836 12.01 12.01 C
ATOM 4572 O LYS C 151 65.493 37.600 112.882 16.00 16.00 O
ATOM 4573 CB LYS C 151 65.144 33.970 113.358 12.01 12.01 C
ATOM 4574 CG LYS C 151 65.912 32.877 114.088 12.01 12.01 C
ATOM 4575 CD LYS C 151 67.128 32.399 113.304 12.01 12.01 C
ATOM 4576 CE LYS C 151 67.638 31.055 113.817 12.01 12.01 C
ATOM 4577 NZ LYS C 151 68.536 30.367 112.845 14.01 14.01 N
ATOM 4578 N PRO C 152 63.957 36.119 111.972 14.01 14.01 N
ATOM 4579 CA PRO C 152 63.508 37.232 111.112 12.01 12.01 C
ATOM 4580 C PRO C 152 63.109 38.448 111.934 12.01 12.01 C
ATOM 4581 O PRO C 152 63.440 39.574 111.564 16.00 16.00 O
ATOM 4582 CB PRO C 152 62.297 36.661 110.371 12.01 12.01 C
ATOM 4583 CG PRO C 152 62.611 35.226 110.237 12.01 12.01 C
ATOM 4584 CD PRO C 152 63.111 34.901 111.606 12.01 12.01 C
ATOM 4585 N ALA C 153 62.412 38.211 113.040 14.01 14.01 N
ATOM 4586 CA ALA C 153 61.963 39.291 113.912 12.01 12.01 C
ATOM 4587 C ALA C 153 63.098 40.266 114.150 12.01 12.01 C
ATOM 4588 O ALA C 153 63.069 41.394 113.658 16.00 16.00 O
ATOM 4589 CB ALA C 153 61.447 38.743 115.234 12.01 12.01 C
ATOM 4590 N TYR C 154 64.115 39.823 114.883 14.01 14.01 N
ATOM 4591 CA TYR C 154 65.267 40.665 115.165 12.01 12.01 C
ATOM 4592 C TYR C 154 65.756 41.261 113.864 12.01 12.01 C
ATOM 4593 O TYR C 154 66.400 42.302 113.847 16.00 16.00 O
ATOM 4594 CB TYR C 154 66.376 39.866 115.831 12.01 12.01 C
ATOM 4595 CG TYR C 154 67.016 40.606 116.973 12.01 12.01 C
ATOM 4596 CD2 TYR C 154 67.159 40.015 118.220 12.01 12.01 C
ATOM 4597 CD1 TYR C 154 67.468 41.902 116.804 12.01 12.01 C
ATOM 4598 CE2 TYR C 154 67.743 40.697 119.266 12.01 12.01 C
ATOM 4599 CE1 TYR C 154 68.055 42.593 117.842 12.01 12.01 C
ATOM 4600 CZ TYR C 154 68.190 41.987 119.072 12.01 12.01 C
ATOM 4601 OH TYR C 154 68.775 42.675 120.111 16.00 16.00 O
ATOM 4602 N GLY C 155 65.432 40.583 112.771 14.01 14.01 N
ATOM 4603 CA GLY C 155 65.788 41.039 111.449 12.01 12.01 C
ATOM 4604 C GLY C 155 65.033 42.277 111.006 12.01 12.01 C
ATOM 4605 O GLY C 155 64.881 43.241 111.751 16.00 16.00 O
ATOM 4606 N GLN C 156 64.550 42.233 109.773 14.01 14.01 N
ATOM 4607 CA GLN C 156 63.853 43.353 109.162 12.01 12.01 C
ATOM 4608 C GLN C 156 62.850 43.968 110.123 12.01 12.01 C
ATOM 4609 O GLN C 156 62.506 45.141 110.012 16.00 16.00 O
ATOM 4610 CB GLN C 156 63.138 42.899 107.894 12.01 12.01 C
ATOM 4611 CG GLN C 156 64.021 42.114 106.945 12.01 12.01 C
ATOM 4612 CD GLN C 156 63.662 40.645 106.916 12.01 12.01 C
ATOM 4613 OE1 GLN C 156 62.516 40.271 107.160 16.00 16.00 O
ATOM 4614 NE2 GLN C 156 64.642 39.802 106.616 14.01 14.01 N
ATOM 4615 N ALA C 157 62.387 43.173 111.075 14.01 14.01 N
ATOM 4616 CA ALA C 157 61.412 43.650 112.046 12.01 12.01 C
ATOM 4617 C ALA C 157 61.892 44.877 112.817 12.01 12.01 C
ATOM 4618 O ALA C 157 61.110 45.516 113.514 16.00 16.00 O
ATOM 4619 CB ALA C 157 61.039 42.537 113.014 12.01 12.01 C
ATOM 4620 N LYS C 158 63.168 45.211 112.703 14.01 14.01 N
ATOM 4621 CA LYS C 158 63.684 46.365 113.420 12.01 12.01 C
ATOM 4622 C LYS C 158 63.183 47.677 112.829 12.01 12.01 C
ATOM 4623 O LYS C 158 62.833 48.598 113.561 16.00 16.00 O
ATOM 4624 CB LYS C 158 65.215 46.350 113.441 12.01 12.01 C
ATOM 4625 CG LYS C 158 65.885 46.986 112.230 12.01 12.01 C
ATOM 4626 CD LYS C 158 67.364 47.232 112.484 12.01 12.01 C
ATOM 4627 CE LYS C 158 67.585 48.021 113.764 12.01 12.01 C
ATOM 4628 NZ LYS C 158 67.696 47.123 114.945 14.01 14.01 N
ATOM 4629 N TYR C 159 63.215 47.748 111.504 14.01 14.01 N
ATOM 4630 CA TYR C 159 62.848 48.954 110.776 12.01 12.01 C
ATOM 4631 C TYR C 159 61.362 49.227 110.625 12.01 12.01 C
ATOM 4632 O TYR C 159 60.808 50.102 111.288 16.00 16.00 O
ATOM 4633 CB TYR C 159 63.486 48.914 109.383 12.01 12.01 C
ATOM 4634 CG TYR C 159 64.927 48.468 109.382 12.01 12.01 C
ATOM 4635 CD2 TYR C 159 65.676 48.472 110.547 12.01 12.01 C
ATOM 4636 CD1 TYR C 159 65.540 48.048 108.213 12.01 12.01 C
ATOM 4637 CE2 TYR C 159 66.996 48.072 110.545 12.01 12.01 C
ATOM 4638 CE1 TYR C 159 66.858 47.646 108.202 12.01 12.01 C
ATOM 4639 CZ TYR C 159 67.578 47.660 109.370 12.01 12.01 C
ATOM 4640 OH TYR C 159 68.888 47.260 109.362 16.00 16.00 O
END
"""
m = multimer(reconstruction_type = 'ba', pdb_str=pdb_str)
assert m.new_annotation is not None
assert m.new_annotation.get_n_helices() == 24, \
"expecing 24 helices, got %d" % m.new_annotation.get_n_helices()
assert m.new_annotation.get_n_sheets() == 0, \
"expecing 0 sheets, got %d" % m.new_annotation.get_n_helices()
def __init__(self,
n_macro_cycle,
sites,
u_iso,
transformations,
finite_grad_differences_test,
use_geometry_restraints,
shake_site_mean_distance = 1.5,
d_min = 2,
shake_angles_sigma = 0.035,
shake_translation_sigma = 0.5):
""" create temp test files and data for tests """
adopt_init_args(self, locals())
self.test_files_names = [] # collect names of files for cleanup
# 1 NCS copy: starting template to generate whole asu; place into P1 box
pdb_inp = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
pdb_obj = iotbx.pdb.hierarchy.input(pdb_string=ncs_1_copy)
mtrix_object = pdb_inp.process_mtrix_records()
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
xrs_one_ncs = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
ph.adopt_xray_structure(xrs_one_ncs)
of = open("one_ncs_in_asu.pdb", "w")
print >> of, mtrix_object.as_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs_one_ncs.crystal_symmetry())
of.close()
# 1 NCS copy -> full asu (expand NCS). This is the answer-structure
m = multimer(file_name="one_ncs_in_asu.pdb",
round_coordinates=False,
reconstruction_type='cau',error_handle=True,eps=1e-2)
assert m.number_of_transforms == 2, m.number_of_transforms
xrs_asu = m.assembled_multimer.extract_xray_structure(
crystal_symmetry = xrs_one_ncs.crystal_symmetry())
m.write("full_asu.pdb")
# force ASU none-rounded coordinates into xray structure
xrs_asu.set_sites_cart(m.sites_cart())
assert xrs_asu.crystal_symmetry().is_similar_symmetry(
xrs_one_ncs.crystal_symmetry())
# Generate Fobs from answer structure
f_obs = abs(xrs_asu.structure_factors(d_min=d_min, algorithm="direct").f_calc())
r_free_flags = f_obs.generate_r_free_flags()
mtz_dataset = f_obs.as_mtz_dataset(column_root_label="F-obs")
mtz_dataset.add_miller_array(
miller_array=r_free_flags,
column_root_label="R-free-flags")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name = "data.mtz")
# Shake structure - subject to refinement input
xrs_shaken = xrs_one_ncs.deep_copy_scatterers()
if sites: xrs_shaken.shake_sites_in_place(
mean_distance=shake_site_mean_distance)
if self.u_iso:
u_random = flex.random_double(xrs_shaken.scatterers().size())
xrs_shaken = xrs_shaken.set_u_iso(values=u_random)
if self.transformations:
transforms_obj = ncs.input(
transform_info = mtrix_object,
pdb_hierarchy_inp = pdb_obj)
x = nu.concatenate_rot_tran(transforms_obj=transforms_obj)
x = nu.shake_transformations(
x = x,
shake_angles_sigma=self.shake_angles_sigma,
shake_translation_sigma=self.shake_translation_sigma)
transforms_obj = nu.update_rot_tran(x=x,transforms_obj=transforms_obj)
mtrix_object = transforms_obj.build_MTRIX_object()
ph.adopt_xray_structure(xrs_shaken)
of = open("one_ncs_in_asu_shaken.pdb", "w")
print >> of, mtrix_object.as_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs.crystal_symmetry())
of.close()
self.f_obs = f_obs
self.r_free_flags = r_free_flags
self.xrs_one_ncs = xrs_one_ncs
# Get restraints manager
self.grm = None
pdb_str = m.assembled_multimer.as_pdb_string(
crystal_symmetry=xrs_one_ncs.crystal_symmetry())
self.iso_restraints = None
if(self.use_geometry_restraints):
self.grm = nu.get_restraints_manager(pdb_string=pdb_str)
if(self.u_iso):
temp = mmtbx.refinement.adp_refinement.adp_restraints_master_params
self.iso_restraints = temp.extract().iso
def run():
# 1 NCS copy: starting template to generate whole asu; place into P1 box
pdb_inp = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
mtrix_object = pdb_inp.process_mtrix_records()
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
xrs_one_ncs = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
ph.adopt_xray_structure(xrs_one_ncs)
open("one_ncs_in_asu.pdb", "w").write(ncs_1_copy)
#of = open("one_ncs_in_asu.pdb", "w")
#print >> of, mtrix_object.format_MTRIX_pdb_string()
#print >> of, ph.as_pdb_string(crystal_symmetry=xrs_one_ncs.crystal_symmetry())
#of.close()
# 1 NCS copy -> full asu (expand NCS). This is the answer-strucure
m = multimer("one_ncs_in_asu.pdb",'cau',error_handle=True,eps=1e-2)
m.write("full_asu_2.pdb")
pdb_inp = iotbx.pdb.input(file_name="full_asu_2.pdb")
xrs = pdb_inp.xray_structure_simple()
xrs_one_asu = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=2)
#xrs_one_asu = xrs.cubic_unit_cell_around_centered_scatterers(
#buffer_size=1)
crystal_symmetry = xrs_one_asu.crystal_symmetry()
#crystal_symmetry = xrs.crystal_symmetry()
xrs_asu = m.assembled_multimer.extract_xray_structure(
crystal_symmetry = crystal_symmetry)
#ph = pdb_inp.construct_hierarchy()
#ph.adopt_xray_structure(xrs_one_asu)
pdb_inp_2 = iotbx.pdb.input(file_name="one_ncs_in_asu.pdb")
pdb_inp_2.write_pdb_file(file_name = "one_ncs_in_asu.pdb",
crystal_symmetry = crystal_symmetry)
#of = open("one_ncs_in_asu.pdb", "w")
#print >> of, mtrix_object.format_MTRIX_pdb_string()
#print >> of, ph.as_pdb_string(crystal_symmetry=xrs_one_asu.crystal_symmetry())
#of.close()
#m = multimer("one_ncs_in_asu.pdb",'cau',error_handle=True,eps=1e-2)
m.write("full_asu_2.pdb")
assert m.number_of_transforms == 2
#xrs_asu = m.assembled_multimer.extract_xray_structure(
#crystal_symmetry = xrs_one_ncs.crystal_symmetry())
#m.write("full_asu.pdb")
assert xrs_asu.crystal_symmetry().is_similar_symmetry(
xrs_one_ncs.crystal_symmetry())
# Generate Fobs from answer structure
f_obs = abs(xrs_asu.structure_factors(d_min=2, algorithm="direct").f_calc())
r_free_flags = f_obs.generate_r_free_flags()
mtz_dataset = f_obs.as_mtz_dataset(column_root_label="F-obs")
mtz_dataset.add_miller_array(
miller_array=r_free_flags,
column_root_label="R-free-flags")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name = "data.mtz")
# Shake structure - subject to refinement input
xrs_shaken = xrs_one_ncs.deep_copy_scatterers()
xrs_shaken.shake_sites_in_place(mean_distance=0.3)
#ph.adopt_xray_structure(xrs_shaken)
of = open("one_ncs_in_asu_shaken.pdb", "w")
print >> of, mtrix_object.format_MTRIX_pdb_string()
