Hi David,
I would do something like this:
$ cat tst.py
def run(mtz):
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(mtz).as_miller_arrays()
for ma in miller_arrays: print ma.info().labels
fobs = [ma for ma in miller_arrays if ma.info().labels == ['F', 'SIGF']]
fc = [ma for ma in miller_arrays if ma.info().labels == ['FC_ALL', 'PHIC_ALL']]
assert len(fobs) == 1, len(fobs)
assert len(fc) == 1, len(fc)
fobs = fobs[0]
fc = fc[0]
fobs.show_summary()
fc.show_summary()
if __name__ == '__main__':
import sys
run(sys.argv[1])
$ dials.python tst.py dimple/final.mtz
['FreeR_flag']
['F', 'SIGF']
['FC', 'PHIC']
['FC_ALL', 'PHIC_ALL']
['FWT', 'PHWT']
['DELFWT', 'PHDELWT']
['FOM']
['FC_ALL_LS', 'PHIC_ALL_LS']
Miller array info: dimple/final.mtz:F,SIGF
Observation type: xray.amplitude
Type of data: double, size=14217
Type of sigmas: double, size=14217
Number of Miller indices: 14217
Anomalous flag: False
Unit cell: (68.2317, 68.2317, 108.095, 90, 90, 90)
Space group: P 43 21 2 (No. 96)
Miller array info: dimple/final.mtz:FC_ALL,PHIC_ALL
Observation type: None
Type of data: complex_double, size=14551
Type of sigmas: None
Number of Miller indices: 14551
Anomalous flag: False
Unit cell: (68.2317, 68.2317, 108.095, 90, 90, 90)
Space group: P 43 21 2 (No. 96)
Cheers,
Richard
Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078
Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
________________________________
From: [email protected] on behalf of David Waterman
Sent: 14 August 2018 11:37:29
To: cctbx mailing list
Subject: [cctbxbb] Extracting data from MTZ
Hi all,
I have a script that extracts Fobs and Fcalc from an MTZ file produced by Refmac for some analysis. I was just doing this in a trivial way:
fobs = m.extract_reals("F").data
fc = m.extract_reals("FC_ALL").data
and this worked fine, until I came across a file with missing observations, so that the lengths of fobs and fc do not match.
Can anybody advise a better way to do this please? I'm inexperienced with iotbx.mtz. I don't need anything other than the values of the structure factors, but I need each element of fobs and fc to contain the equivalent values.
Thanks
-- David
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