dials.reindex

Introduction

This program can be used to re-index an indexed.expt and/or indexed.refl 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 indexed.expt 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 ambiguity, a reference dataset (models.expt and reflection.refl) 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 indexed.expt change_of_basis_op=b+c,a+c,a+b

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

dials.reindex indexed.expt indexed.refl change_of_basis_op=l,h,k

dials.reindex indexed.expt indexed.refl reference.experiments=reference.expt
  reference.reflections=reference.refl

Basic parameters

change_of_basis_op = a,b,c
hkl_offset = None
space_group = None
reference {
  experiments = None
  reflections = None
}
output {
  experiments = reindexed.expt
  reflections = reindexed.refl
}

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.expt
    .help = "The filename for reindexed experimental models"
    .type = str
  reflections = reindexed.refl
    .help = "The filename for reindexed reflections"
    .type = str
}