Using xia2

As mentioned in the quick start guide, to get started simply run:

xia2 pipeline=dials /here/are/my/images

or:

xia2 pipeline=3d /here/are/my/images

The program is used from the command-line; there is no GUI. The most important command-line options are as follows:

Option	Usage
atom= X	tell xia2 to separate anomalous pairs i.e. I(+) \(\neq\) I(−) in scaling
pipeline=dials	tell xia2 to use DIALS with DIALS scaling
pipeline=dials-aimless	tell xia2 to use DIALS and Aimless
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

These specify in the broadest possible terms to the program the manner in which you would like the processing performed. The program will then read all of the image headers found in /here/are/my/data to organise the data, first into sweeps, then into wavelengths, before assigning all of these wavelengths to a crystal.

The data from the experiment is understood as follows. The SWEEP, which corresponds to one “scan”, is the basic unit of indexing and integration. These are contained by WAVELENGTH objects which correspond to CCP4 MTZ datasets, and will ultimately have unique Miller indices. For example, a low and high dose pass will be merged together. A CRYSTAL however contains all of the data from the experiment and is the basic unit of data for scaling. This description of the experiment is written automatically to an instruction file, an example of which is shown in below:

BEGIN PROJECT AUTOMATIC
BEGIN CRYSTAL DEFAULT

BEGIN HA_INFO
ATOM Ba
END HA_INFO

BEGIN WAVELENGTH SAD
WAVELENGTH 0.979500
END WAVELENGTH SAD

BEGIN SWEEP SWEEP1
WAVELENGTH SAD
DIRECTORY /dls/i02/data/2011/mx1234-5
IMAGE K5_M1S3_3_001.img
START_END 1 450
END SWEEP SWEEP1

END CRYSTAL DEFAULT
END PROJECT AUTOMATIC

The input file to the program, which is generated automatically, shows how the input data are understood. This may be adjusted and the program rerun, which will be covered in more detail later in the manual.