def lattice_test(integrate_lp, xds_inp_file):
images, phi, cell, records = rj_parse_integrate_lp(
open(integrate_lp).readlines())
# next work through the XDS.INP file to get the proper name template
# out...
nt = None
distance = None
for record in open(xds_inp_file, 'r').readlines():
if 'NAME_TEMPLATE_OF_DATA_FRAMES' in record:
nt = record.strip()
if 'DETECTOR_DISTANCE' in record:
distance = record.strip()
if not nt:
raise RuntimeError, 'filename template not found in %s' % xds_inp_file
if not distance:
raise RuntimeError, 'distance not found in %s' % xds_inp_file
r_new = [distance]
for r in records:
if not 'NAME_TEMPLATE_OF_DATA_FRAMES' in r:
r_new.append(r)
else:
r_new.append(nt)
records = r_new
# ok, in here need to rerun XDS with all of the data from all of
# the images and the triclinic target cell, then parse out the
# solutions from the CORRECT.LP file (applying the cell constants -
# done in the parser) and then use *these* as the target, as the
# lattice symmetry code (interestingly) does not always give the
# right answer...
standard = [
'JOB=CORRECT',
'MAXIMUM_NUMBER_OF_PROCESSORS=4',
'CORRECTIONS=!',
'REFINE(CORRECT)=CELL',
'OVERLOAD=65000',
'DIRECTION_OF_DETECTOR_X-AXIS=1.0 0.0 0.0',
'DIRECTION_OF_DETECTOR_Y-AXIS=0.0 1.0 0.0',
'TRUSTED_REGION=0.0 1.41'
]
# first get the list of possible lattices - do this by running CORRECT
# with all of the images, then looking at the favourite settings for the
# P1 result (or something) - meh.
fout = open('XDS.INP', 'w')
for record in standard:
fout.write('%s\n' % record)
for record in records:
fout.write('%s\n' % record)
fout.write('DATA_RANGE= %d %d\n' % images)
fout.write('OSCILLATION_RANGE= %.2f\n' % phi)
fout.write(
'UNIT_CELL_CONSTANTS= %.2f %.2f %.2f %.2f %.2f %.2f\n' % tuple(cell))
fout.write('SPACE_GROUP_NUMBER=%d\n' % 1)
fout.close()
output = rj_run_job('xds_par', [], [])
# read CORRECT.LP to get the right solutions...
result = rj_parse_xds_correct_lp(open('CORRECT.LP', 'r').readlines())
for lattice in result:
cp = '%.2f %.2f %.2f %.2f %.2f %.2f' % result[lattice]['cell']
# print '%s %s' % (lattice, cp)
# result = lattice_symmetry(cell)
lattices = sort_lattices(result)
# then iterate through them...
data = { }
for l in lattices:
data[l] = { }
c = result[l]['cell']
fout = open('XDS.INP', 'w')
for record in standard:
fout.write('%s\n' % record)
for record in records:
fout.write('%s\n' % record)
fout.write('DATA_RANGE= %d %d\n' % (images))
fout.write('OSCILLATION_RANGE= %.2f\n' % phi)
fout.write(
'UNIT_CELL_CONSTANTS= %.2f %.2f %.2f %.2f %.2f %.2f\n' % tuple(c))
fout.write('SPACE_GROUP_NUMBER=%d\n' % lattice_spacegroup(l))
fout.close()
output = rj_run_job('xds_par', [], [])
# now read out the records I want from CORRECT.LP...
rmsd = None
rmsp = None
for record in open('CORRECT.LP').readlines():
if 'STANDARD DEVIATION OF SPOT POSITION' in record:
rmsd = float(record.split()[-1])
if 'STANDARD DEVIATION OF SPINDLE POSITION' in record:
rmsp = float(record.split()[-1])
if not rmsp or not rmsd:
raise RuntimeError, 'refinement failed'
print '%s rmsd %f rmsp %f' % (l, rmsd, rmsp)
def lattice_test(integrate_lp, xds_inp_file):
images, phi, cell, records = rj_parse_integrate_lp(
open(integrate_lp).readlines())
# next work through the XDS.INP file to get the proper name template
# out...
nt = None
distance = None
for record in open(xds_inp_file, 'r').readlines():
if 'NAME_TEMPLATE_OF_DATA_FRAMES' in record:
nt = record.strip()
if 'DETECTOR_DISTANCE' in record:
distance = record.strip()
if not nt:
raise RuntimeError, 'filename template not found in %s' % xds_inp_file
if not distance:
raise RuntimeError, 'distance not found in %s' % xds_inp_file
r_new = [distance]
for r in records:
if not 'NAME_TEMPLATE_OF_DATA_FRAMES' in r:
r_new.append(r)
else:
r_new.append(nt)
records = r_new
# ok, in here need to rerun XDS with all of the data from all of
# the images and the triclinic target cell, then parse out the
# solutions from the CORRECT.LP file (applying the cell constants -
# done in the parser) and then use *these* as the target, as the
# lattice symmetry code (interestingly) does not always give the
# right answer...
standard = [
'JOB=CORRECT',
'MAXIMUM_NUMBER_OF_PROCESSORS=4',
'CORRECTIONS=!',
'REFINE(CORRECT)=CELL',
'OVERLOAD=65000',
'DIRECTION_OF_DETECTOR_X-AXIS=1.0 0.0 0.0',
'DIRECTION_OF_DETECTOR_Y-AXIS=0.0 1.0 0.0',
'TRUSTED_REGION=0.0 1.41'
]
# first get the list of possible lattices - do this by running CORRECT
# with all of the images, then looking at the favourite settings for the
# P1 result (or something) - meh.
fout = open('XDS.INP', 'w')
for record in standard:
fout.write('%s\n' % record)
for record in records:
fout.write('%s\n' % record)
fout.write('DATA_RANGE= %d %d\n' % images)
fout.write('OSCILLATION_RANGE= %.2f\n' % phi)
fout.write(
'UNIT_CELL_CONSTANTS= %.2f %.2f %.2f %.2f %.2f %.2f\n' % tuple(cell))
fout.write('SPACE_GROUP_NUMBER=%d\n' % 1)
fout.close()
output = rj_run_job('xds_par', [], [])
# read CORRECT.LP to get the right solutions...
result = rj_parse_xds_correct_lp(open('CORRECT.LP', 'r').readlines())
for lattice in result:
cp = '%.2f %.2f %.2f %.2f %.2f %.2f' % result[lattice]['cell']
# print '%s %s' % (lattice, cp)
# result = lattice_symmetry(cell)
lattices = sort_lattices(result)
# then iterate through them...
data = { }
for l in lattices:
data[l] = { }
c = result[l]['cell']
# print 'Lattice: %s' % l
# print 'Cell: %.2f %.2f %.2f %.2f %.2f %.2f' % tuple(c)
# then iterate through the image ranges
w = nint(10.0/phi)
m = nint((images[1] - images[0] + 1) / w)
for j in range(m):
start = j * w + 1
end = j * w + w
data[l][j] = { }
fout = open('XDS.INP', 'w')
for record in standard:
fout.write('%s\n' % record)
for record in records:
fout.write('%s\n' % record)
fout.write('DATA_RANGE= %d %d\n' % (start, end))
fout.write('OSCILLATION_RANGE= %.2f\n' % phi)
fout.write(
'UNIT_CELL_CONSTANTS= %.2f %.2f %.2f %.2f %.2f %.2f\n' % tuple(c))
fout.write('SPACE_GROUP_NUMBER=%d\n' % lattice_spacegroup(l))
fout.close()
output = rj_run_job('xds_par', [], [])
# now read out the records I want from CORRECT.LP...
rmsd = None
rmsp = None
for record in open('CORRECT.LP').readlines():
if 'STANDARD DEVIATION OF SPOT POSITION' in record:
rmsd = float(record.split()[-1])
if 'STANDARD DEVIATION OF SPINDLE POSITION' in record:
rmsp = float(record.split()[-1])
if not rmsp or not rmsd:
raise RuntimeError, 'refinement failed'
data[l][j] = {'d':rmsd,
'p':rmsp}
# now tabulate the results
for j in range(m):
record = '%d' % j
for l in lattices[1:]:
record += ' %.3f %.3f' % (data[l][j]['d'] / data['aP'][j]['d'],
data[l][j]['p'] / data['aP'][j]['p'])
print record
# now print out the averages, sd's
recordm = 'M'
records = 'S'
sigma = { }
for l in lattices[1:]:
values = [(data[l][j]['d'] / data['aP'][j]['d']) for j in range(m)]
md, sd = meansd(values)
values = [(data[l][j]['p'] / data['aP'][j]['p']) for j in range(m)]
mp, sp = meansd(values)
recordm += ' %.3f %.3f' % (md, mp)
records += ' %.3f %.3f' % (sd, sp)
sigma[l] = { }
if sd > 0:
sigma[l]['d'] = ((md - 1) / sd)
else:
sigma[l]['d'] = 0.0
if sp > 0:
sigma[l]['p'] = ((mp - 1) / sp)
else:
sigma[l]['p'] = 0.0
print recordm
print records
for l in lattices[1:]:
d = sigma[l]['d']
p = sigma[l]['p']
print '= %s %.3f %.3f' % (l, d, p)
