xia2.ssx_reduce

xia2.ssx_reduce is an autoprocessing pipeline that merges data from multiple SSX collections.

The xia2.ssx_reduce pipeline is triggered automatically on still-shot data collections on I24 if they are specified as being part of the same sample group. To specify sample groups, a "sample_groups.yml" file is created in the processing directory at:

and contains the names of the collections (e.g. fixed target chips) in each sample group in a line in the file in this format:

where "chip1" etc. should be replaced with the actual names used for the data collections.

Here, chips 1-3 form a sample group, while chips 4-7 form a different sample group. Datasets are merged together only if they are part of the same sample group. Typically different sample groups correspond to different sample preparation conditions or measurement conditions.

Once a xia2.ssx job has completed, if the collection is named in the sample_groups.yml, and there is more than one processed collection in that group, a separate xia2.ssx_reduce job is triggered. This job takes as input the integrated data from all completed xia2.ssx jobs from collections in that group. This xia2.ssx_reduce job performs the data reduction part of xia2.ssx on the dataset as a whole, using dials.cosym program to resolve indexing ambiguities, if these are allowed by the space group symmetry or cell parameters, before scaling and merging the data.

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.ssx_reduce log is the "xia2.ssx_reduce.log" file. A merging HTML report, named dials.merge.html is generated, which contains a more extensive set of data quality statistics and plots. The main data output datafile from xia2.ssx_reduce is the "merged.mtz" file, which is cut to the approximate resolution limit. A separate merged MTZ file, "merged_full.mtz", contains data to the full resolution limit of the detector.

If your publication uses data processed with the xia2.ssx_reduce pipeline, please cite the following reference:

• Beilsten-Edmands, James, et al. "Processing serial synchrotron crystallography diffraction data with DIALS." Methods in Enzymology. Vol. 709. Academic Press, 2024. 207-244.

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

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