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. Alternatively, to reindex an integated dataset in the case of indexing abiguity, a reference dataset (experiments.json and reflection.pickle) in the same space group can be specified. In this case, any potential twin operators are tested, and the dataset is reindexed to the setting that gives the highest correlation with the reference dataset.

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

dials.reindex experiments.json index.pickle reference.experiments=ref_experiments.json
  reference.reflections=ref_reflections.pickle

Basic parameters

change_of_basis_op = a,b,c
hkl_offset = None
space_group = None
reference {
  experiments = None
  reflections = 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 {
  experiments = None
    .help = "Reference experiment for determination of change of basis"
            "operator."
    .type = path
  reflections = None
    .help = "Reference reflections to allow reindexing to consistent index"
            "between datasets."
    .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
}