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.
See also: phenix.xtriage
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