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Open-source tools for serial crystallographic 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) or a synchrotron. Built on the Computational Crystallographic Toolbox (cctbx), the same toolbox on which PHENIX, DIALS, LABELIT, and post-refinement and merging program, PRIME are built, it enables the user to solve difficult problems relating to processing serial crystallographic 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), SACLA, the European XFEL, or a synchrotron, 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. Finally, processing approaches for data collection at non-LCLS sources are also provided.

• Overview to the system architecture at LCLS and real-time progress monitoring of data processing
• Installation: there are two ways to get cctbx.xfel:
  • cctbx.xfel is installed for general use at SLAC. To start using an existing installation, simply source the current build.
  • Download a binary bundle of DIALS. Use this option if you will not be processing LCLS data because, for example, if you have serial crystallographic data from a synchrotron.
  • Build a psana/cctbx.xfel build from scratch. Use this option if you want to process LCLS data outside of LCLS or want your own build.
• Tutorials on pre-processing, data reduction, and merging.
• cctbx.prime: tutorials on post-refinement using PRIME.
• IOTA: tutorial on spotfinding optimization using IOTA.

Other related information:

• Serial XFEL Crystallography References
• Data Processing at SACLA
• Indexing individual stills: how to index stills not necessarily from an XFEL source.
• Processing Blog describing how we solved typical problems.
• Processing L498 thermolysin details instructions to reproduce the results published in the forthcoming cctbx.xfel paper.
• 2017 Tutorials. Berkeley Lab Serial Crystallography Workshop, 16-17 Feb 2017.
• 2014 Workshop Tutorial: cctbx.xfel . Note, due to recent changes at LCLS, many of these tutorials are out of date for data collected late 2014 and onwards. For more up to date information, see above tutorials. For data collected before late 2014, these workshop tutorials are useful.
• Powerpoint presentations
• 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.
• File formats: for developers, information on file formats cctbx.xfel uses
• Cppxfel: XFEL data processing with the CPPXFEL package from Diamond/Wellcome Trust.
• For developers only: Installation instructions for cctbx developmental build.

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