As mentioned in the quick start guide, to get started simply run:
xia2 pipeline=dials /here/are/my/images
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:
tell xia2 to separate anomalous pairs i.e. I(+) \(\neq\) I(−) in scaling
tell xia2 to use DIALS with DIALS scaling
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.