Reflection Statistics

phenix.reflection_statistics

Comparisions between multiple datasets are available via the phenix.reflection_statistics command:

Usage: phenix.reflection_statistics [options] reflection_file [...]

Options:
  -h, --help            show this help message and exit
  --unit-cell=10,10,20,90,90,120|FILENAME
                        External unit cell parameters
  --space-group=P212121|FILENAME
                        External space group symbol
  --symmetry=FILENAME   External file with symmetry information
  --weak-symmetry       symmetry on command line is weaker than symmetry found
                        in files
  --quick               Do not compute statistics between pairs of data arrays
  --resolution=FLOAT    High resolution limit (minimum d-spacing, d_min)
  --low-resolution=FLOAT
                        Low resolution limit (maximum d-spacing, d_max)
  --bins=INT            Number of bins
  --bins-twinning-test=INT
                        Number of bins for twinning test
  --bins-second-moments=INT
                        Number of bins for second moments of intensities
  --lattice-symmetry-max-delta=LATTICE_SYMMETRY_MAX_DELTA
                        angular tolerance in degrees used in the determination
                        of the lattice symmetry

Example: phenix.reflection_statistics data1.mtz data2.sca

This utility reads one or more reflection files (many common formats incl. MTZ, Scalepack, CNS, SHELX). For each of the datasets found in the reflection files the output shows a block like the following:

Miller array info: gere_MAD.mtz:FSEinfl,SIGFSEinfl,DSEinfl,SIGDSEinfl
Observation type: xray.reconstructed_amplitude
Type of data: double, size=20994
Type of sigmas: double, size=20994
Number of Miller indices: 20994
Anomalous flag: 1
Unit cell: (108.742, 61.679, 71.652, 90, 97.151, 90)
Space group: C 1 2 1 (No. 5)
Systematic absences: 0
Centric reflections: 0
Resolution range: 24.7492 2.74876
Completeness in resolution range: 0.873513
Completeness with d_max=infinity: 0.872315
Bijvoet pairs: 10497
Lone Bijvoet mates: 0
Anomalous signal: 0.1065

This is followed by a listing of the completeness and the anomalous signal in resolution bins. The number of bins and the resolution range may be adjusted with the options shown above.

Unless the --quick option is specified the output will also show the correlations between the datasets and, if applicable, between the anomalous differences, both as overall values and in bins. The correlation between anomalous differences is often a very powerful indicator for the resolution up to which the anomalous signal is useful for substructure determination.