dials.reindex

Introduction

This program can be used to re-index an experiments.json and/or indexed.pickle file from one setting to another. The change of basis operator can be provided in h,k,l, or a,b,c or x,y,z conventions. By default the change of basis operator will also be applied to the space group in the experiments.json file, however, optionally, a space group (including setting) to be applied AFTER applying the change of basis operator can be provided.

Examples:

dials.reindex experiments.json change_of_basis_op=b+c,a+c,a+b

dials.reindex indexed.pickle change_of_basis_op=-b,a+b+2*c,-a

dials.reindex experiments.json index.pickle change_of_basis_op=l,h,k

Basic parameters

change_of_basis_op = a,b,c
hkl_offset = None
space_group = None
reference = None
output {
  experiments = reindexed_experiments.json
  reflections = reindexed_reflections.pickle
}

Full parameter definitions

change_of_basis_op = a,b,c
  .type = str
hkl_offset = None
  .type = ints(size=3)
space_group = None
  .help = "The space group to be applied AFTER applying the change of basis "
          "operator."
  .type = space_group
reference = None
  .help = "Reference experiment for determination of change of basis operator."
  .type = path
output {
  experiments = reindexed_experiments.json
    .help = "The filename for reindexed experimental models"
    .type = str
  reflections = reindexed_reflections.pickle
    .help = "The filename for reindexed reflections"
    .type = str
}