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

WAVELENGTH 0.979500