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Open-source tools for free-electron laser data processing

cctbx.xfel is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL). Built on the Computational Crystallographic Toolbox (cctbx), the same toolbox on which PHENIX and LABELIT are built, it enables the user to solve difficult problems relating to processing XFEL data. The programs and modules provided by cctbx.xfel can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source (LCLS) to a single MTZ file containing merged reflection intensities suitable for structure solution.


cctbx.xfel resources

The tutorials on this wiki provide detailed instructions for indexing and integrating still diffraction images extracted from the raw data streams recorded at the LCLS, including pre-processing steps such as dark pedestal generation and refinement of the detector geometry of the Cornell–SLAC pixel array detectors (CSPAD) in use at the CXI and XPP end stations. The tutorials also cover tools to efficiently leverage the LCLS computing cluster to process the thousands to millions of diffraction images that can be recorded in a short time.

  • Overview to the system architecture at LCLS and real-time progress monitoring of data processing
  • Installation: cctbx.xfel is installed for general use at SLAC. To start using an existing installation, first set up the PSDM software distribution and then set up cctbx.xfel.
    • To install cctbx.xfel elsewhere, or to set up an installation for development purposes, see the Installation instructions. For most regular users this should not be necessary; SLAC as well as several other sites already have a generally accessible installation.
    • Maintaining an installation describes how to keep a setup up-to-date.
  • Tutorials on pre-processing, data reduction, and merging.
  • Processing Blog describing how we solved typical problems.
  • Processing L498 thermolysin details instructions to reproduce the results published in the forthcoming cctbx.xfel paper.

This project is under active development. For any assistance, please contact the authors.

Serial XFEL Crystallography References

Experiment-day guidelines: a short, very hands-on set of notes for online monitoring and data-processing using cctbx.xfel. This page assumes that the setup and tutorial have been completed.

Indexing individual stills: how to index still not necessarily from an XFEL source.