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 models.expt observations.refl

Basic parameters

d_min = Auto
min_i_mean_over_sigma_mean = 4
min_cc_half = 0.6
normalisation = kernel quasi ml_iso *ml_aniso
lattice_group = None
seed = 230
lattice_symmetry_max_delta = 2.0
relative_length_tolerance = 0.05
absolute_angle_tolerance = 2
partiality_threshold = 0.4
laue_group = auto
change_of_basis_op = None
best_monoclinic_beta = True
systematic_absences {
  check = True
  significance_level = *0.95 0.975 0.99
}
output {
  log = dials.symmetry.log
  experiments = "symmetrized.expt"
  reflections = "symmetrized.refl"
  json = dials.symmetry.json
  html = "dials.symmetry.html"
}

Full parameter definitions

exclude_images = None
  .help = "Input in the format exp:start:end Exclude a range of images (start,"
          "stop) from the dataset with experiment identifier exp  (inclusive"
          "of frames start, stop)."
  .type = strings
  .multiple = True
  .expert_level = 1
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)
normalisation = kernel quasi ml_iso *ml_aniso
  .type = choice
lattice_group = None
  .type = space_group
seed = 230
  .type = int(value_min=0, allow_none=True)
lattice_symmetry_max_delta = 2.0
  .type = float(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 = 0.4
  .help = "Use only reflections with a partiality above this threshold."
  .type = float(allow_none=True)
laue_group = auto
  .help = "Optionally specify the Laue group. If set to auto, then test all"
          "possible  Laue groups. If set to None, then take the Laue group"
          "from the input file."
  .type = space_group
change_of_basis_op = None
  .type = str
best_monoclinic_beta = True
  .help = "If True, then for monoclinic centered cells, I2 will be preferred"
          "over C2 if it gives a less oblique cell (i.e. smaller beta angle)."
  .type = bool
systematic_absences {
  check = True
    .help = "Check systematic absences for the current laue group."
    .type = bool
  significance_level = *0.95 0.975 0.99
    .help = "Signficance to use when testing whether axial reflections are "
            "different to zero (absences and reflections in reflecting"
            "condition)."
    .type = choice
}
output {
  log = dials.symmetry.log
    .type = str
  experiments = "symmetrized.expt"
    .type = path
  reflections = "symmetrized.refl"
    .type = path
  json = dials.symmetry.json
    .type = path
  html = "dials.symmetry.html"
    .help = "Filename for html report."
    .type = path
}