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News! See our [[https://doi.org/10.1101/2025.05.04.652045 new preprint]]! This paper shows current best practices using ''cctbx.xfel'' with ''DIALS'' for serial crystallographic data. | |||
= 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 ([https://cctbx.github.io/ ''cctbx'']), the same toolbox on which [http://www.phenix-online.org ''PHENIX''], and [http://dials.github.io DIALS] 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 ([http://lcls.slac.stanford.edu LCLS]), [http://sacla.xfel.jp SACLA], the [https://www.xfel.eu/ European XFEL], or a synchrotron, to a single MTZ file containing merged reflection intensities suitable for structure solution. | ||
* [// | == ''cctbx.xfel'' resources == | ||
* [https:// | |||
* [// | The current best resource is our pre-print, [https://doi.org/10.1101/2025.05.04.652045 ''cctbx.xfel: a suite for processing serial crystallographic data.'']. This paper describes the algorithms and ideas behind the implementation and execution of the two main programs of ''cctbx.xfel'': | ||
* ''dials.stills_process'': this program runs through all the first steps of processing data using dials: import (reading image headers), spot finding, indexing, geometry refinement, and integration. Serial images are independent from each other, so this program is optimized for massively parallel systems, but can be adapted to a variety of single and multi-processing modes. | |||
* ''cctbx.xfel.merge'': this program runs through the remaining steps of processing: scaling and merging to produce a full dataset (.mtz file). For documentation, see our [https://github.com/cctbx/cctbx_project/tree/master/xfel/merging Github project] | |||
Additional resources: | |||
* Our [http://cci.lbl.gov/publications/download/CCN_2019_p22_Brewster.pdf 2019 newsletter article] describes how to use the ''cctbx.xfel'' GUI, an interactive program for handling large XFEL datasets. | |||
* [[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, [[Using the pre-built cctbx at LCLS|simply source the current build]]. | |||
** [https://dials.github.io/installation.html 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 [https://exafel.github.io/docs/psana-cctbx-install 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. | |||
Other related information: | |||
* [[Serial XFEL Crystallography References]] | |||
This project is under active development. For any assistance, please contact the authors. | |||
Latest revision as of 21:14, 15 July 2026
News! See our [new preprint]! This paper shows current best practices using cctbx.xfel with DIALS for serial crystallographic data.
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, and DIALS 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 current best resource is our pre-print, cctbx.xfel: a suite for processing serial crystallographic data.. This paper describes the algorithms and ideas behind the implementation and execution of the two main programs of cctbx.xfel:
- dials.stills_process: this program runs through all the first steps of processing data using dials: import (reading image headers), spot finding, indexing, geometry refinement, and integration. Serial images are independent from each other, so this program is optimized for massively parallel systems, but can be adapted to a variety of single and multi-processing modes.
- cctbx.xfel.merge: this program runs through the remaining steps of processing: scaling and merging to produce a full dataset (.mtz file). For documentation, see our Github project
Additional resources:
- Our 2019 newsletter article describes how to use the cctbx.xfel GUI, an interactive program for handling large XFEL datasets.
- 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.
Other related information:
This project is under active development. For any assistance, please contact the authors.