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(+) I(−) in scaling
-2d	tell xia2 to use MOSFLM and Aimless
-3d	tell xia2 to use XDS and XSCALE
-3dii	tell xia2 to use XDS and XSCALE, indexing with peaks found from all images
-dials	tell xia2 to use DIALS and Aimless
-xinfo	modified.xinfo use specific input file
-image /path/to/an/image.img	process specific scan
-small molecule	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

Resolution limits

The subject of resolution limits is one often raised - by default in xia2 they are:

• Merged
• Unmerged

However you can override these with -misigma, -isigma

Phil parameters

Note

We are currently moving 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 are 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

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 {
  check_image_files_readable = True
}
xds {
  delphi = 5
  delphi_small = 30
  untrusted_ellipse = None
  untrusted_rectangle = None
  trusted_region = None
  profile_grid_size = None
  correct {
    refine = *DISTANCE *BEAM *AXIS *ORIENTATION *CELL *POSITION
  }
  integrate {
    refine = *ORIENTATION *CELL *BEAM *DISTANCE AXIS *POSITION
    refine_final = *ORIENTATION *CELL BEAM DISTANCE AXIS POSITION
    fix_scale = False
    delphi = 0
    reflecting_range = 0
    reflecting_range_esd = 0
    beam_divergence = 0
    beam_divergence_esd = 0
    reintegrate = true
  }
  init {
    fix_scale = False
  }
  index {
    refine = *ORIENTATION *CELL *BEAM *DISTANCE *AXIS *POSITION
    debug = *OFF ON
  }
  colspot {
    minimum_pixels_per_spot = 1
  }
  xscale {
    min_isigma = 3.0
  }
  merge2cbf {
    merge_n_images = 2
    data_range = None
    moving_average = False
  }
}
dials {
  fix_geometry = False
  outlier.algorithm = null *auto mcd tukey sauter_poon
  fast_mode = False
  find_spots {
    min_spot_size = Auto
    min_local = 0
    phil_file = None
    sigma_strong = None
    filter_ice_rings = False
    kernel_size = 3
    global_threshold = None
  }
  index {
    method = fft1d *fft3d real_space_grid_search
    phil_file = None
    max_cell = 0.0
    use_all_reflections = False
    fft3d.n_points = None
  }
  refine {
    scan_varying = True
    interval_width_degrees = 36.0
    use_all_reflections = True
    phil_file = None
    reflections_per_degree = 100
  }
  integrate {
    phil_file = None
    profile_fitting = True
    background_outlier_algorithm = *null nsigma truncated normal tukey mosflm
    background_algorithm = simple null *glm
    use_threading = False
    include_partials = True
  }
}
ccp4 {
  truncate {
    program = 'ctruncate'
  }
  reindex {
    program = 'pointless'
  }
  aimless {
    intensities = summation profile *combine
    surface_tie = 0.001
    surface_link = True
  }
}
xia2.settings {
  input {
    image = None
    json = None
    reference_geometry = None
    reverse_phi = False
    xinfo = None
    gain = None
    min_images = 10
    min_oscillation_range = None
  }
  sweep {
    id = None
    range = None
    exclude = False
  }
  scale {
    directory = Auto
  }
  unit_cell = None
  space_group = None
  d_min = None
  d_max = None
  optimize_scaling = False
  unify_setting = False
  beam_centre = None
  trust_beam_centre = False
  wavelength_tolerance = 0.00001
  read_all_image_headers = True
  detector_distance = None
  show_template = False
  untrusted_rectangle_indexing = None
  xds_cell_deviation = 0.05, 5.0
  use_brehm_diederichs = False
  developmental {
    use_dials_spotfinder = False
    pointless_tolerance = 0.0
  }
  integrate_p1 = False
  reintegrate_correct_lattice = True
  xds {
    geometry_x = None
    geometry_y = None
  }
  indexer = mosflm labelit labelitii xds xdsii xdssum dials
  refiner = mosflm xds dials
  integrater = mosflmr xdsr mosflm xds dials
  scaler = ccp4a xdsa
  verbose = False
  multiprocessing {
    mode = *serial parallel
    nproc = Auto
    njob = Auto
    type = *simple qsub
    qsub_command = ''
  }
}