def generateMap(nativePdb, nativeMtz):
logging.debug("Parsing MTZ file %s to determine column labels", nativeMtz)
F, SIGF, FREE = mtz_util.get_labels(nativeMtz)
logging.debug("Generating map from: %s %s", nativeMtz, nativePdb)
return phenixer.generateMap(nativeMtz,
nativePdb,
FP=F,
SIGFP=SIGF,
FREE=FREE)
def test_process_mtz_labels2(self):
# Get MTZ flags
os.chdir(self.thisd) # Need as otherwise tests that happen in other directories change os.cwd()
mtz = os.path.join( self.testfiles_dir, "1dtx.mtz" )
FP,SIGFP,FREE=mtz_util.get_labels(mtz)
self.assertEqual(FP,'FP')
self.assertEqual(SIGFP,'SIGFP')
self.assertEqual(FREE,'FreeR_flag')
def test_process_mtz_labels(self):
# Get MTZ flags
os.chdir(
self.thisd
) # Need as otherwise tests that happen in other directories change os.cwd()
mtz = os.path.join(self.testfiles_dir, "2uui_sigmaa.mtz")
FP, SIGFP, FREE = mtz_util.get_labels(mtz)
self.assertEqual(FP, 'F')
self.assertEqual(SIGFP, 'SIGF')
self.assertEqual(FREE, None)
required=True)
parser.add_argument('-native_pdb',
help="Input native PDB file",
required=False)
parser.add_argument('-f_label',
help="F label from native MTZ file",
required=False)
parser.add_argument('-sigf_label',
help="SIGF label from native MTZ file",
required=False)
args = parser.parse_args()
# Extract F & SIGF from file if not give on command-line
if args.f_label and args.sigf_label:
f_label, sigf_label = args.f_label, args.sigf_label
else:
f_label, sigf_label, _ = mtz_util.get_labels(args.native_mtz)
_logger.info("Using F, SIGF labels from mtz file: {0}, {1} ".format(
f_label, sigf_label))
if args.native_pdb:
before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_pdb(
args.native_pdb, args.native_mtz, args.mr_mtz, f_label, sigf_label)
else:
before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_mtz(
args.native_mtz, args.mr_mtz, f_label, sigf_label)
print "Calculated phase error: {0}".format(after_origin)
print "Calculated origin shift: {0}".format(origin_shift)
import argparse
parser = argparse.ArgumentParser(description='Run cphasematch on two mtz files', prefix_chars="-")
parser.add_argument('-native_mtz', help="Input native MTZ file", required=True)
parser.add_argument('-mr_mtz', help="Input MTZ file from Molecular Replacement", required=True)
parser.add_argument('-native_pdb', help="Input native PDB file", required=False)
parser.add_argument('-f_label', help="F label from native MTZ file", required=False)
parser.add_argument('-sigf_label', help="SIGF label from native MTZ file", required=False)
args = parser.parse_args()
# Extract F & SIGF from file if not give on command-line
if args.f_label and args.sigf_label:
f_label, sigf_label = args.f_label, args.sigf_label
else:
f_label, sigf_label, _ = mtz_util.get_labels(args.native_mtz)
logger.info("Using F, SIGF labels from mtz file: {0}, {1} ".format(f_label, sigf_label))
if args.native_pdb:
before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_pdb(
args.native_pdb, args.native_mtz, args.mr_mtz, f_label, sigf_label
)
else:
before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_mtz(
args.native_mtz, args.mr_mtz, f_label, sigf_label
)
print("Calculated phase error:", after_origin)
print("Calculated origin shift:", origin_shift)