dials.export

Introduction

This program is used to export the results of dials processing in various formats.

The output formats currently supported are:

MTZ format exports the files as an unmerged mtz file, ready for input to downstream programs such as Pointless and Aimless. For exporting integrated, but unscaled data, the required input is a models.expt file and an integrated.refl file. For exporting scaled data, the required input is a models.expt file and a scaled.pickle file, also passing the option intensity=scale.

NXS format exports the files as an NXmx file. The required input is a models.expt file and an integrated.refl file.

MMCIF format exports the files as an mmcif file. The required input is a models.expt file and an integrated.refl file.

XDS_ASCII format exports intensity data and the experiment metadata in the same format as used by the output of XDS in the CORRECT step - output can be scaled with XSCALE.

SADABS format exports intensity data (and geometry by direction cosines) as an ersatz-SADABS format reverse engineered from the file format used by EvalCCD for input to SADABS.

MOSFLM format exports the files as an index.mat mosflm-format matrix file and a mosflm.in file containing basic instructions for input to mosflm. The required input is an models.expt file.

XDS format exports a models.expt file as XDS.INP and XPARM.XDS files. If a reflection pickle is given it will be exported as a SPOT.XDS file.

Examples:

# Export to mtz
dials.export models.expt integrated.refl
dials.export models.expt integrated.refl mtz.hklout=integrated.mtz
dials.export models.expt scaled.pickle intensity=scale mtz.hklout=scaled.mtz

# Export to nexus
dials.export models.expt integrated.refl format=nxs
dials.export models.expt integrated.refl format=nxs nxs.hklout=integrated.nxs

# Export to mmcif
dials.export models.expt integrated.refl format=mmcif
dials.export models.expt integrated.refl format=mmcif mmcif.hklout=integrated.mmcif

# Export to mosflm
dials.export models.expt integrated.refl format=mosflm

# Export to xds
dials.export strong.pickle format=xds
dials.export indexed.pickle format=xds
dials.export models.expt format=xds
dials.export models.expt indexed.pickle format=xds

Basic parameters

format = *mtz sadabs nxs mmcif mosflm xds xds_ascii json
intensity = *auto profile sum scale
debug = False
mtz {
  combine_partials = True
  partiality_threshold = 0.4
  min_isigi = -5
  force_static_model = False
  filter_ice_rings = False
  d_min = None
  hklout = auto
  crystal_name = XTAL
  project_name = DIALS
  best_unit_cell = None
}
sadabs {
  hklout = integrated.sad
  run = 1
  predict = False
}
xds_ascii {
  hklout = DIALS.HKL
}
nxs {
  hklout = integrated.nxs
  instrument_name = Unknown
  instrument_short_name = Unknown
  source_name = Unknown
  source_short_name = Unknown
}
mmcif {
  hklout = auto
}
mosflm {
  directory = mosflm
}
xds {
  directory = xds
}
json {
  filename = rlp.json
  compact = True
  n_digits = 6
}
output {
  log = dials.export.log
}

Full parameter definitions

format = *mtz sadabs nxs mmcif mosflm xds xds_ascii json
  .help = "The output file format"
  .type = choice
intensity = *auto profile sum scale
  .help = "Choice of which intensities to export. Allowed combinations:
      "
          "     scale, profile, sum, profile+sum, sum+profile+scale. Auto"
          "will
            default to scale or profile+sum depending on if"
          "the data are scaled."
  .type = choice(multi=True)
debug = False
  .help = "Output additional debugging information"
  .type = bool
mtz {
  combine_partials = True
    .help = "Combine partials that have the same partial id into one
       "
            "reflection, with an updated partiality given by the sum of the
  "
            "     individual partialities."
    .type = bool
  partiality_threshold = 0.4
    .help = "All reflections with partiality values above the partiality
     "
            "  threshold will be retained. This is done after any combination"
            "of
        partials if applicable."
    .type = float(allow_none=True)
  min_isigi = -5
    .help = "Exclude reflections with unfeasible values of I/Sig(I)"
    .type = float(allow_none=True)
  force_static_model = False
    .help = "Force program to use static model even if scan varying is present"
    .type = bool
  filter_ice_rings = False
    .help = "Filter reflections at ice ring resolutions"
    .type = bool
  d_min = None
    .help = "Filter out reflections with d-spacing below d_min"
    .type = float(allow_none=True)
  hklout = auto
    .help = "The output MTZ filename, defaults to integrated.mtz or"
            "scaled_unmerged.mtz depending on if the input data are scaled."
    .type = path
  crystal_name = XTAL
    .help = "The name of the crystal, for the mtz file metadata"
    .type = str
  project_name = DIALS
    .help = "The project name for the mtz file metadata"
    .type = str
  best_unit_cell = None
    .help = "Best unit cell value, to use when performing resolution cutting,"
            "and as the overall unit cell in the exported mtz. If None, the"
            "median cell will be used."
    .type = unit_cell
}
sadabs {
  hklout = integrated.sad
    .help = "The output raw sadabs file"
    .type = path
  run = 1
    .help = "Batch number / run number for output file"
    .type = int(allow_none=True)
  predict = False
    .help = "Compute centroids with static model, not observations"
    .type = bool
}
xds_ascii {
  hklout = DIALS.HKL
    .help = "The output raw hkl file"
    .type = path
}
nxs {
  hklout = integrated.nxs
    .help = "The output Nexus file"
    .type = path
  instrument_name = Unknown
    .help = "Name of the instrument/beamline"
    .type = str
  instrument_short_name = Unknown
    .help = "Short name for instrument/beamline, perhaps the acronym"
    .type = str
  source_name = Unknown
    .help = "Name of the source/facility"
    .type = str
  source_short_name = Unknown
    .help = "Short name for source, perhaps the acronym"
    .type = str
}
mmcif {
  hklout = auto
    .help = "The output CIF file, defaults to integrated.cif or"
            "scaled_unmerged.cif
        depending on if the data are scaled."
    .type = path
}
mosflm {
  directory = mosflm
    .help = "The output directory for mosflm output"
    .type = path
}
xds {
  directory = xds
    .help = "The output directory for xds output"
    .type = path
}
json {
  filename = rlp.json
    .type = path
  compact = True
    .type = bool
  n_digits = 6
    .help = "Number of decimal places to be used for representing the"
            "reciprocal lattice points."
    .type = int(value_min=1, allow_none=True)
}
output {
  log = dials.export.log
    .help = "The log filename"
    .type = path
}