xia2-3dii

xia2-3dii is an autoprocessing pipeline that uses the XDS software package to perform the steps of data processing.

The xia2-3dii pipeline is triggered automatically on rotation data collections. Some information from the sample information page is used to determine what options to run xia2 with. If a space group is associated with the sample, two instances of the xia2 pipeline will be run, one with the space group specified and one without. If an anomalous scatterer is specified in the "Anomalous Scatterer" field (e.g. "Se"), xia2 will be run with the option "atom=Se", which tells xia2 to separate anomalous pairs in scaling, which can be essential for crystals containing strongly absorbing atoms such as metals. Note that the name of the atom itself does not affect the processing, rather its presence is just used to switch anomalous separation on or off. Finally, if a unit cell is specified, this will also be used in the xia2 pipeline.

Reprocessing options

When reprocessing data via the "Reprocess Data" view in ISPyB, further options can be specified, including high and low resolution limits, threshold levels for determining the resolution cutoff (CC Half, Unmerged I/sigma, Merged I/sigma).

The small molecule option processes data in a manner more suited to small molecule/chemical crystallography data, including outputting data in formats suitable for direct structure solution programs (shelx). The absorption level and indexing method options are not used in the xia2-3dii pipeline.

Viewing results

A summary view of the main processing statistics is displayed in ISPyB. The "Logs & Files" button displays a list of processing logfiles and datafiles for the individual processing steps. The main xia2 log is the "xia2.txt" file; the exact program options used when running xia2 can be found near the top of this file. xia2 also generates an interactive HTML report, named xia2.html, which contains a more extensive set of data quality statistics and plots. The main data output datafile from xia2 is the file ending in "_free.mtz" - this is a merged MTZ file containing free-R flags that can be taken on for downstream structure determination.

If your publication uses data processed with the xia2-3dii pipeline, please cite the following references:

• Winter, Graeme. "xia2: an expert system for macromolecular crystallography data reduction." Applied Crystallography 43.1 (2010): 186-190.
• Kabsch, Wolfgang. "xds." Biological crystallography 66.2 (2010): 125-132.

If you deposit a structure in the PDB which is determined from data processed with the xia2-3dii pipeline, please make sure both xia2 and XDS are included in the software category.

The documentation for xia2 can be found here: https://xia2.github.io

The documentation for xds can be found here: https://xds.mr.mpg.de