Parameters

Commonly used program options

There are a number of program options used on a daily basis in xia2, which are:

atom=X	Tell xia2 to separate anomalous pairs i.e. I(+) \(\neq\) I(−) in scaling.
pipeline=3d	Tell xia2 to use XDS and XSCALE.
pipeline=3dii	Tell xia2 to use XDS and XSCALE, indexing with peaks found from all images.
pipeline=dials	Tell xia2 to use DIALS.
pipeline=dials-aimless	Tell xia2 to use DIALS but scale with Aimless.
xinfo=some.xinfo	Use specific modified .xinfo input file.
image=/path/to/an/image.img	Process a specific scan. Pass multiple image= parameters to include multiple scans.
image=/path/to/an/image.img:start:end	Process a specific image range within a scan. start and end are numbers denoting the image range, e.g. image=/path/to/an/image.img:1:100 processes images 1–100 inclusive. As above, one can pass multiple image= parameters.
small_molecule=true	Process in manner more suited to small molecule data.
space_group=sg	Set the spacegroup, e.g. P21.
unit_cell=a,b,c,α,β,γ	Set the cell constants.
hdf5_plugin=/path/to/durin.so	Set the path to the HDF5 file reading plugin for XDS (needed for processing of Eiger data)

Resolution limits

xia2 uses dials.estimate_resolution to estimate the resolution limit, sharing the same parameters and defaults. The default behaviour (cc_half=0.3) can be overridden with e.g.:

xia2 [options] cc_half=None misigma=1 isigma=0.25

See the dials.estimate_resolution documentation for further details.

Phil parameters

Note

We have now moved towards moving PHIL (Python-based Hierarchial Interchange Language) for specifying xia2 program parameters, which will in the long run help the documentation, but in the mean time you may see some warnings as certain parameters were changed from -param style parameters to param= style PHIL parameters. If you see, e.g.:

Warning: -spacegroup option deprecated: please use space_group='P422' instead

Warning: -resolution option deprecated: please use d_min=1.5 instead

Command line option -3d is deprecated. Please use pipeline=3d instead

don’t panic - this is to be expected - but you may want to change the way you run xia2 or your scripts. More of a warning for beamline / automation people! The outcome of this should however be automated generation of command-line documentation and the ability to keep “recipes” for running xia2 in tidy files.

Here is a comprehensive list of PHIL parameters used by xia2:

general {
}
xds {
  keep_outliers = True
  correct {
  }
  integrate {
  }
  init {
  }
  defpix {
  }
  index {
    max_wedge_size = 5
    max_wedge_size_degrees = None
  }
  colspot {
  }
  xscale {
  }
  merge2cbf {
  }
}
dials {
  outlier {
  }
  detect_blanks {
    phi_step = 2
    counts_fractional_loss = 0.1
    misigma_fractional_loss = 0.1
  }
  find_spots {
    filter_ice_rings = False
  }
  index {
    method = fft1d *fft3d real_space_grid_search
    max_cell_estimation {
    }
  }
}
xia2.settings {
  pipeline = 3d 3dd 3di 3dii *dials dials-aimless
  project = 'AUTOMATIC'
  crystal = 'DEFAULT'
  input {
    atom = None
    anomalous = Auto
  }
  space_group = None
  unit_cell = None
  resolution {
    keep_all_reflections = Auto
    d_max = None
    d_min = None
    cc_half_method = *half_dataset sigma_tau
    reflections_per_bin = 10
    labels = None
    reference = None
    emax = 4
  }
  multiprocessing {
    nproc = Auto
  }
  symmetry {
    chirality = chiral nonchiral centrosymmetric
    program = *pointless dials
  }
  output {
    mmcif {
    }
  }
}