def __init__(self, cell, symmetry, sg_number, dmin, dmax, columns,
filename):
assert isinstance(columns[0], tuple)
Cell.__init__(self, cell, symmetry)
self.sg_number = sg_number
self.dmin = dmin
self.dmax = dmax
assert dmin >= dmax # yes, min > max here
self.columns = OrderedDict(columns)
self.filename = filename
def __init__(self, cell, symmetry, sg_number, dmin, dmax, columns,
filename):
assert isinstance(columns[0], tuple)
Cell.__init__(self, cell, symmetry)
self.sg_number = sg_number
self.dmin = dmin
self.dmax = dmax
assert dmin >= dmax # yes, min > max here
self.columns = OrderedDict(columns)
self.filename = filename
def __init__(self, cryst1_line):
assert cryst1_line.startswith("CRYST1")
a = float(cryst1_line[6:15])
b = float(cryst1_line[15:24])
c = float(cryst1_line[24:33])
alpha = float(cryst1_line[33:40])
beta = float(cryst1_line[40:47])
gamma = float(cryst1_line[47:54])
symmetry = cryst1_line[55:66].strip()
Cell.__init__(self, (a, b, c, alpha, beta, gamma), symmetry)
self.has_hetatm_x = None
def __init__(self, cryst1_line):
assert cryst1_line.startswith('CRYST1')
a = float(cryst1_line[6:15])
b = float(cryst1_line[15:24])
c = float(cryst1_line[24:33])
alpha = float(cryst1_line[33:40])
beta = float(cryst1_line[40:47])
gamma = float(cryst1_line[47:54])
symmetry = cryst1_line[55:66].strip()
Cell.__init__(self, (a, b, c, alpha, beta, gamma), symmetry)
self.has_hetatm_x = None
class TestCell(unittest.TestCase):
def setUp(self):
self.cell = Cell((22.84, 32.84, 42.84, 80.84, 90.84, 100.84), None)
def test_orth(self):
orth = self.cell.get_orth_matrix()
expected = np.array([[22.84, -6.17612, -0.628045],
[0, 32.254, 6.82343],
[0, 0, 42.2884]])
assert_allclose(to_np(orth), expected, rtol=1e-6)
def test_frac(self):
frac = self.cell.get_frac_matrix()
orth = self.cell.get_orth_matrix()
assert_allclose(to_np(frac.dot(orth)), np.identity(3), atol=1e-12)
def dimple(wf, opt):
comment(' ### Dimple v%s. Problems and suggestions:'
' ccp4.github.io/dimple ###' % __version__)
mtz_meta = wf.read_mtz_metadata(opt.mtz)
_comment_summary_line('MTZ (%.1fA)' % mtz_meta.dmax, mtz_meta)
if opt.dls_naming:
opt.pdbs = dls_name_filter(opt.pdbs)
opt.pdbs = utils.filter_out_duplicate_files(opt.pdbs, relto=opt.output_dir)
if not opt.pdbs:
comment('\nNo non-empty pdb files given. Nothing to do.')
return
for p in opt.pdbs:
wf.read_pdb_metadata(p, print_errors=(len(opt.pdbs) > 1))
if len(opt.pdbs) > 1:
comment('\nPDBs in order of similarity (using the first one):')
opt.pdbs.sort(
key=lambda x: calculate_difference(wf.file_info[x], mtz_meta))
utils.log_value('data_file', opt.mtz)
utils.log_value('pdb_files', opt.pdbs)
for p in opt.pdbs:
_comment_summary_line(os.path.basename(p), wf.file_info[p])
ini_pdb = 'ini.pdb'
wf.copy_uncompressed(opt.pdbs[0], ini_pdb)
pdb_meta = wf.file_info[opt.pdbs[0]]
if pdb_meta is None:
put_error('PDB file missing CRYST1 record, starting from MR')
if opt.no_hetatm or check_hetatm_x(wf.path(ini_pdb), pdb_meta):
if not opt.no_hetatm:
comment('\nHETATM marked as element X would choke many programs.')
rb_xyzin = 'prepared.pdb'
wf.temporary_files.add(rb_xyzin)
n_het = wf.remove_hetatm(xyzin=ini_pdb,
xyzout=rb_xyzin,
remove_all=opt.no_hetatm)
comment('\nRemoved %d HETATM atoms' % n_het)
else:
rb_xyzin = ini_pdb
# run rwcontents even without CRYST1 - it will show mol. weight only
wf.rwcontents(xyzin=rb_xyzin).run()
rw_data = wf.jobs[-1].data
if pdb_meta is None:
pass # we already had a warning message
elif rw_data.get('solvent_percent') is None:
put_error('rwcontents could not interpret %s' % rb_xyzin)
elif rw_data['solvent_percent'] > HIGH_SOLVENT_PCT:
comment('\nHmm... %.1f%% of solvent or incomplete model' %
rw_data['solvent_percent'])
if abs(wf.jobs[-1].data.get('volume', 0) - pdb_meta.get_volume()) > 10:
comment('\ndebug: problem when calculating volume?')
####### pointless - reindexing #######
if match_symmetry(mtz_meta, pdb_meta) and opt.mr_when_r > 0 and (
0.7 < mtz_meta.get_volume() / pdb_meta.get_volume() < 1.4):
reindexed_mtz = 'pointless.mtz'
wf.temporary_files.add(reindexed_mtz)
wf.pointless(hklin=opt.mtz,
xyzin=rb_xyzin,
hklout=reindexed_mtz,
keys='TOLERANCE 5').run(may_fail=True)
alt_reindex = wf.jobs[-1].data.get('alt_reindex')
if wf.jobs[-1].exit_status == 0 and alt_reindex:
for ar in alt_reindex:
comment('\n %-10s CC: %-8.3f cell diff: %.1fA' %
(ar['op'], ar['cc'], ar['cell_deviat']))
else:
# until recently (2015) pointless didn't print CC for non-ambiguous
# spacegroups (e.g. C2), but now it always prints
comment('\n no good indexing')
reindexed_mtz = opt.mtz
else:
reindexed_mtz = opt.mtz
reindexed_mtz_meta = wf.read_mtz_metadata(reindexed_mtz)
if reindexed_mtz_meta.symmetry != mtz_meta.symmetry:
_comment_summary_line('reindexed MTZ', reindexed_mtz_meta)
####### (c)truncate - calculate amplitudes if needed #######
if not opt.fcolumn:
opt.fcolumn = 'F' if 'F' in mtz_meta.columns else 'FP'
elif opt.icolumn or opt.ItoF_prog:
put_error('Ignoring options --fcolumn/--sigfcolumn')
opt.sigfcolumn = opt.sigfcolumn.replace('<FCOL>', opt.fcolumn)
if (opt.ItoF_prog or opt.icolumn or opt.fcolumn not in mtz_meta.columns
or opt.sigfcolumn not in mtz_meta.columns):
f_mtz = 'amplit.mtz'
wf.temporary_files.add(f_mtz)
i_sigi_cols = _find_i_sigi_columns(mtz_meta, opt)
if opt.ItoF_prog == 'ctruncate' or (opt.ItoF_prog is None
and opt.slow):
colano = None
if opt.anode and all(
col in mtz_meta.columns
for col in ['I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)']):
colano = '/*/*/[I(+),SIGI(+),I(-),SIGI(-)]'
wf.ctruncate(hklin=reindexed_mtz,
hklout=f_mtz,
colin='/*/*/[%s,%s]' % i_sigi_cols,
colano=colano).run()
else:
wf.truncate(hklin=reindexed_mtz,
hklout=f_mtz,
labin='IMEAN=%s SIGIMEAN=%s' % i_sigi_cols,
labout='F=F SIGF=SIGF').run()
opt.fcolumn = 'F'
opt.sigfcolumn = 'SIGF'
else:
f_mtz = reindexed_mtz
####### rigid body - check if model is good for refinement? #######
refmac_labin_nofree = 'FP=%s SIGFP=%s' % (opt.fcolumn, opt.sigfcolumn)
refmac_xyzin = None
cell_diff = calculate_difference(pdb_meta, reindexed_mtz_meta)
if pdb_meta is None:
pass # the error message was already printed
elif opt.mr_when_r <= 0:
comment('\nMR requested unconditionally.')
elif cell_diff > 0.1 and opt.mr_when_r < 1:
comment('\nDifferent unit cells.')
elif pdb_meta.symmetry != reindexed_mtz_meta.symmetry:
comment('\nDifferent space groups.')
else:
comment('\nRigid-body refinement with resolution 3.5 A, %d cycles.' %
opt.rigid_cycles)
if 'aa_count' in rw_data and 'water_count' in rw_data:
if rw_data['aa_count'] != 0:
comment(' %.1f waters/aa.' %
(rw_data['water_count'] / rw_data['aa_count']))
else:
comment(' %d/0 waters/aa.' % rw_data['water_count'])
wf.temporary_files |= {'refmacRB.pdb', 'refmacRB.mtz'}
# it may fail because of "Disagreement between mtz and pdb"
wf.refmac5(hklin=f_mtz,
xyzin=rb_xyzin,
hklout='refmacRB.mtz',
xyzout='refmacRB.pdb',
labin=refmac_labin_nofree,
libin=None,
keys="""refinement type rigidbody resolution 15 3.5
rigidbody ncycle %d""" %
opt.rigid_cycles).run(may_fail=True)
# if the error is caused by mtz/pdb disagreement, continue with MR
if wf.jobs[-1].exit_status != 0:
comment('\nTry MR.')
elif not wf.jobs[-1].data.get('overall_r'):
comment('\nWARNING: unknown R factor, something went wrong.\n')
refmac_xyzin = 'refmacRB.pdb'
elif wf.jobs[-1].data['overall_r'] > opt.mr_when_r:
comment('\nRun MR for R > %g.' % opt.mr_when_r)
else:
comment('\nNo MR for R < %g.' % opt.mr_when_r)
refmac_xyzin = 'refmacRB.pdb'
####### phaser/molrep - molecular replacement #######
if refmac_xyzin is None:
vol_ratio = None
if pdb_meta:
# num_mol accounts for strict NCS (MTRIX without iGiven)
vol_ratio = (mtz_meta.asu_volume() /
pdb_meta.asu_volume(rw_data['num_mol']))
comment(' Volume of asu: %.1f%% of model asu.' % (100 * vol_ratio))
if opt.mr_when_r >= 1:
comment('\nWould try MR, but it is disabled.')
return
if opt.mr_num:
mr_num = opt.mr_num
else:
mr_num = guess_number_of_molecules(mtz_meta, rw_data, vol_ratio)
mw = rw_data.get('weight')
if isinstance(mr_num, float):
wf.ensembler(pdbin=rb_xyzin, root='ens').run()
n_models = len(wf.jobs[-1].data['models'])
mw = None
rb_xyzin = 'ens_merged.pdb'
mr_num = max(int(round(mr_num * n_models)), 1)
# phaser is used by default if number of searched molecules is known
if opt.mr_prog == 'molrep':
wf.temporary_files |= {
'molrep.pdb', 'molrep_dimer.pdb', 'molrep.crd'
}
wf.molrep(f=f_mtz, m=rb_xyzin).run()
refmac_xyzin = 'molrep.pdb'
else:
wf.temporary_files |= {'phaser.1.pdb', 'phaser.1.mtz'}
wf.phaser_auto(hklin=f_mtz,
labin='F=%s SIGF=%s' %
(opt.fcolumn, opt.sigfcolumn),
model=dict(pdb=rb_xyzin,
identity=100,
num=mr_num,
mw=mw),
sg_alt='ALL',
opt=opt,
root='phaser').run(may_fail=True)
if not _after_phaser_comments(wf.jobs[-1],
sg_in=reindexed_mtz_meta.symmetry):
raise RuntimeError('No phaser solution.')
refmac_xyzin = 'phaser.1.pdb'
f_mtz = 'phaser.1.mtz'
if False:
wf.findwaters(pdbin=refmac_xyzin,
hklin=f_mtz,
f='FC',
phi='PHIC',
pdbout='prepared_wat.pdb',
sigma=2)
refmac_xyzin = 'prepared_wat.pdb'
####### adding free-R flags #######
f_mtz_meta = wf.read_mtz_metadata(f_mtz)
cad_reso = opt.reso or (f_mtz_meta.dmax - MtzMeta.d_eps)
if opt.free_r_flags:
free_mtz = opt.free_r_flags
free_col = check_freerflags_column(wf.path(free_mtz),
expected_symmetry=pdb_meta,
column=opt.freecolumn)
comment('\nFree-R flags from the %s file, column %s.' %
(('reference' if free_mtz != opt.mtz else 'input'), free_col))
else:
free_col = DEFAULT_FREE_COLS[0]
if free_col in f_mtz_meta.columns:
comment('\nReplace free-R flags')
else:
comment('\nGenerate free-R flags')
free_mtz = 'free.mtz'
wf.temporary_files |= {'unique.mtz', free_mtz}
if opt.seed_freerflag or cell_diff > 1e3: # i.e. different SG
wf.unique(hklout='unique.mtz', ref=f_mtz_meta,
resolution=cad_reso).run()
else:
comment(' (repeatably)')
# Here we'd like to have always the same set of free-r flags
# for given PDB file. That's why we don't use information
# from the data file (mtz).
wf.unique(hklout='unique.mtz', ref=pdb_meta, resolution=1.0).run()
# CCP4 freerflag uses always the same pseudo-random sequence by default
wf.freerflag(hklin='unique.mtz',
hklout=free_mtz,
keys=('SEED' if opt.seed_freerflag else '')).run()
if free_mtz == opt.mtz and opt.reso is None:
prepared_mtz = f_mtz
else:
prepared_mtz = 'prepared.mtz'
wf.temporary_files.add(prepared_mtz)
wf.cad(
data_in=[(f_mtz, [c for c in f_mtz_meta.columns if c != free_col]),
(free_mtz, [free_col])],
hklout=prepared_mtz,
keys=[
'sysab_keep', # does it matter?
'reso overall 1000.0 %g' % cad_reso
]).run()
freerflag_missing = wf.count_mtz_missing(prepared_mtz, free_col)
if freerflag_missing:
wf.freerflag(hklin=prepared_mtz,
hklout='prepared2.mtz',
keys='COMPLETE FREE=' + free_col,
parser=' (again, for %d refl. more)' %
freerflag_missing).run()
prepared_mtz = 'prepared2.mtz'
wf.temporary_files.add(prepared_mtz)
####### refinement #######
if opt.weight:
refmac_weight = 'matrix %f' % opt.weight
else:
refmac_weight = 'auto'
restr_ref_keys = """\
make newligand continue
refinement type restrained
weight %s
""" % refmac_weight
if opt.freecolumn_val:
restr_ref_keys += 'free %s\n' % opt.freecolumn_val
refmac_labin = '%s FREE=%s' % (refmac_labin_nofree, free_col)
comment('\nRestrained refinement, %d+%d cycles.' %
(opt.jelly, opt.restr_cycles))
if opt.jelly:
wf.temporary_files |= {'jelly.pdb', 'jelly.mtz'}
wf.refmac5(hklin=prepared_mtz,
xyzin=refmac_xyzin,
hklout='jelly.mtz',
xyzout='jelly.pdb',
labin=refmac_labin,
libin=opt.libin,
keys=restr_ref_keys + 'ridge distance sigma 0.01\n'
'make hydrogen no\n'
'ncycle %d' % opt.jelly + opt.extra_ref_keys).run()
comment(_refmac_rms_line(wf.jobs[-1].data))
refmac_xyzin = 'jelly.pdb'
restr_job = wf.refmac5(
hklin=prepared_mtz,
xyzin=refmac_xyzin,
hklout=opt.hklout,
xyzout=opt.xyzout,
labin=refmac_labin,
libin=opt.libin,
keys=(restr_ref_keys + 'ncycle %d' % opt.restr_cycles +
opt.extra_ref_keys)).run()
comment(_refmac_rms_line(restr_job.data))
# if that run is repeated with --from-step it's useful to compare Rfree
if wf.from_job > 0 and wf.from_job <= len(wf.jobs): # from_job is 1-based
prev = [j for j in wf.repl_jobs if j.name == restr_job.name]
if prev and prev[0].data and 'free_r' in prev[0].data:
comment('\nPreviously: R/Rfree %.4f/%.4f Rfree change: %+.4f' %
(prev[0].data['overall_r'], prev[0].data['free_r'],
restr_job.data['free_r'] - prev[0].data['free_r']))
####### check blobs #######
if opt.blob_search:
if restr_job.data['free_r'] <= BAD_FINAL_RFREE:
fb_job = wf.find_blobs(opt.hklout, opt.xyzout, sigma=0.8).run()
coot_script = _generate_scripts_and_pictures(wf, opt, fb_job.data)
if coot_script:
comment('\nTo see it in Coot run %s' % coot_script)
else:
comment('\nNo blob search for Rfree > %g.' % BAD_FINAL_RFREE)
_generate_scripts_and_pictures(wf, opt, None)
if opt.anode:
# check if mtz contains I+/- and SIGI+/-
column_types = list(reindexed_mtz_meta.columns.values())
if column_types.count('K') != 2 and column_types.count('M') != 2:
comment('\nColumns I+/- and SIG+/- not found. Skipping AnoDe.')
return
anode_name = 'anode'
# convert to sca for input to shelxc
scaout = anode_name + '.sca'
wf.mtz2sca(prepared_mtz, scaout).run()
wf.shelxc(scaout, reindexed_mtz_meta.cell,
reindexed_mtz_meta.symmetry).run()
wf.copy_uncompressed(opt.xyzout, anode_name + '.pdb')
anode_job = wf.anode(anode_name).run()
wf.temporary_files |= {
scaout, anode_name + '.pdb', anode_name + '.hkl',
anode_name + '.pha', anode_name + '_sad.cif',
anode_name + '_fa.hkl'
}
cell = Cell(reindexed_mtz_meta.cell, reindexed_mtz_meta.symmetry)
# need orthogonal not fractional coordinates to generate coot script
anode_job.data['blobs'] = cell.orthogonalize(anode_job.data['xyz'])
comment(_anode_anom_peak_lines(anode_job.data))
coot_script = _generate_scripts_and_pictures(wf,
opt,
anode_job.data,
pha=anode_name + '.pha')
def __init__(self, entry):
Cell.__init__(self, entry[2:8], symmetry=entry[1])
self.pdb_id = entry[0]
self.uniprot_src = entry[8] # we may have a homolog of uniprot entry
def __init__(self, entry):
Cell.__init__(self, entry[2:8], symmetry=entry[1])
self.pdb_id = entry[0]
self.uniprot_src = entry[8] # we may have a homolog of uniprot entry
def setUp(self):
self.cell = Cell((22.84, 32.84, 42.84, 80.84, 90.84, 100.84), None)