[cctbxbb] Extracting data from MTZ

richard.gildea at diamond.ac.uk richard.gildea at diamond.ac.uk
Tue Aug 14 03:54:35 PDT 2018

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]


if __name__ == '__main__':
  import sys

$ dials.python tst.py dimple/final.mtz
['F', 'SIGF']
['FC', 'PHIC']
['FWT', 'PHWT']
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)



Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
OX11 0DE
From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org> on behalf of David Waterman <dgwaterman at gmail.com>
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.


-- David

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