dials.import_xds

Introduction

This program imports xds processed data for use in dials.

It requires up to three things to create an experiment list and reflection table.

• an XDS.INP, to specify the geometry,

• one of “INTEGRATE.HKL” or “XPARM.XDS”, which is needed to create the experiment ( alternatively “XDS_ASCII.HKL” or “GXPARM.XDS” can be specified with xds_file=)

• INTEGRATE.HKL or SPOT.XDS file to create a reflection table.

To run the program, the easiest thing to do is provide a directory containing these files

Example use cases:

dials.import_xds /path/to/folder/containing/xds/inp/                          # Extract all the relevant files from this directory (defaults to importing INTEGRATE.HKL if it exists)

dials.import_xds /path/to/folder/containing/xds/inp/INTEGRATE.HKL             # Specify a path to an INTEGRATE.HKL - the XDS.INP must be in the same directory.

dials.import_xds /path/to/folder/containing/xds/inp/ SPOT.XDS                 # Be explicit about which file to use to create reflections (default is to use INTEGRATE.HKL)

dials.import_xds /path/to/folder/containing/xds/inp/ xds_file=XPARM.XDS       # Specify which extra file should be used to create experiment metadata

dials.import_xds /path/to/folder/containing/xds/inp/ /path/to/INTEGRATE.HKL   # Will take XDS.INP from the directory, and everything else needed from the specified INTEGRATE.HKL file

Basic parameters

input {
  xds_file = None
}
output {
  reflections = None
  xds_experiments = "xds_models.expt"
  log = dials.import_xds.log
}
remove_invalid = False
add_standard_columns = False
read_varying_crystal = False

Full parameter definitions

input {
  xds_file = None
    .help = "Explicitly specify the file to use "
    .type = path
}
output {
  reflections = None
    .help = "The output filname of the reflections file (defaults to either"
            "integrate_hkl.refl or spot_xds.refl)"
    .type = str
  xds_experiments = "xds_models.expt"
    .help = "The output filename of the experiment list created from xds"
    .type = str
  log = dials.import_xds.log
    .type = path
}
remove_invalid = False
  .help = "Remove non-index reflections (if miller indices are present)"
  .type = bool
add_standard_columns = False
  .help = "Add empty standard columns to the reflections. Note columns for"
          "centroid variances are set to contain 1s, not 0s"
  .type = bool
read_varying_crystal = False
  .help = "Attempt to create a scan-varying crystal model from INTEGRATE.LP,"
          "if present"
  .type = bool