dials.symmetry

Introduction

This program implements the methods of POINTLESS ( Evans, P. (2006). Acta Cryst. D62, 72-82. and Evans, P. R. (2011). Acta Cryst. D67, 282-292.) for scoring and determination of Laue group symmetry.

The program takes as input a set of one or more integrated experiments and reflections.

Examples:

dials.symmetry experiments.json reflections.pickle

Basic parameters

d_min = Auto
min_i_mean_over_sigma_mean = 4
min_cc_half = 0.6
batch = None
normalisation = kernel quasi ml_iso *ml_aniso
lattice_group = None
verbosity = 1
seed = 230
relative_length_tolerance = 0.05
absolute_angle_tolerance = 2
partiality_threshold = 0.99
output {
  log = dials.symmetry.log
  debug_log = dials.symmetry.debug.log
  experiments = "reindexed_experiments.json"
  reflections = "reindexed_reflections.pickle"
  json = dials.symmetry.json
}

Full parameter definitions

d_min = Auto
  .type = float(value_min=0, allow_none=True)
min_i_mean_over_sigma_mean = 4
  .type = float(value_min=0, allow_none=True)
min_cc_half = 0.6
  .type = float(value_min=0, value_max=1, allow_none=True)
batch = None
  .type = ints(size=2, value_min=0)
normalisation = kernel quasi ml_iso *ml_aniso
  .type = choice
lattice_group = None
  .type = space_group
verbosity = 1
  .help = "The verbosity level"
  .type = int(value_min=0, allow_none=True)
seed = 230
  .type = int(value_min=0, allow_none=True)
relative_length_tolerance = 0.05
  .type = float(value_min=0, allow_none=True)
absolute_angle_tolerance = 2
  .type = float(value_min=0, allow_none=True)
partiality_threshold = 0.99
  .help = "Use only reflections with a partiality above this threshold."
  .type = float(allow_none=True)
output {
  log = dials.symmetry.log
    .type = str
  debug_log = dials.symmetry.debug.log
    .type = str
  experiments = "reindexed_experiments.json"
    .type = path
  reflections = "reindexed_reflections.pickle"
    .type = path
  json = dials.symmetry.json
    .type = path
}