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dials.check_indexing_symmetry

Introduction

This program can be used to analyse the correlation coefficients between reflections related by the symmetry operators belonging to the space group of the input experiment.json file. It can also check for misindexing of the diffraction pattern, possibly as a result of an incorrect beam centre.

Examples:

dials.check_indexing_symmetry experiment.json indexed.pickle \
  grid=1 symop_threshold=0.7


dials.check_indexing_symmetry experiment.json indexed.pickle \
  grid_l=3 symop_threshold=0.7

Basic parameters

d_min = 0
d_max = 0
symop_threshold = 0
grid = 0
grid_h = 0
grid_k = 0
grid_l = 0
asu = False
normalise = False
normalise_bins = 0
reference = None
output {
  log = dials.check_indexing_symmetry.log
  debug_log = dials.check_indexing_symmetry.debug.log
}

Full parameter definitions

d_min = 0
  .help = "High resolution limit to use for analysis"
  .type = float(allow_none=True)
d_max = 0
  .help = "Low resolution limit to use for analysis"
  .type = float(allow_none=True)
symop_threshold = 0
  .help = "Threshold above which we consider a symmetry operator true."
  .type = float(allow_none=True)
grid = 0
  .help = "Search scope for testing misindexing on h, k, l."
  .type = int(allow_none=True)
grid_h = 0
  .help = "Search scope for testing misindexing on h."
  .type = int(allow_none=True)
grid_k = 0
  .help = "Search scope for testing misindexing on k."
  .type = int(allow_none=True)
grid_l = 0
  .help = "Search scope for testing misindexing on l."
  .type = int(allow_none=True)
asu = False
  .help = "Perform search comparing within ASU (assumes input symm)"
  .type = bool
normalise = False
  .help = "Normalise intensities before calculating correlation coefficients."
  .type = bool
normalise_bins = 0
  .help = "Number of resolution bins for normalisation"
  .type = int(allow_none=True)
reference = None
  .help = "Correctly indexed reference set for comparison"
  .type = path
output {
  log = dials.check_indexing_symmetry.log
    .type = str
  debug_log = dials.check_indexing_symmetry.debug.log
    .type = str
}