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Documentation
About CrystFEL
Welcome to the CrystFEL page!
CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source. CrystFEL comprises programs for indexing and integrating diffraction patterns, scaling and merging intensities, simulating patterns, calculating figures of merit for the data and visualising the results. Supporting scripts are provided to help at all stages, including importing data into CCP4 for further processing.
To begin learning about CrystFEL in more detail, start here.
The primary citation for CrystFEL is as follows. See the list at the end of this page for more references.
T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman. "CrystFEL: a software suite for snapshot serial crystallography". J. Appl. Cryst. 45 (2012), p335–341.
doi:10.1107/S0021889812002312 — Download PDF — Article on IUCr website.
Recent News
- 8 October 2024: CrystFEL version 0.11.1 released. Read the release notes for details. See the download page or the changes page for more information, or watch the accompanying screencast.
- 17 April 2024: CrystFEL version 0.11.0 released. Read the release notes for details. See the download page or the changes page for more information.
- 12 December 2023: The 300th citation for CrystFEL was added to the citation list!
- 20 February 2023: CrystFEL version 0.10.2 released. This is largely a bug-fixing release, but there are also some interesting new features. Read the release notes for details. See the download page or the changes page for more information.
- 14 March 2022: It's CrystFEL's tenth birthday! Read the original announcement of the first public release of CrystFEL on the CCP4bb archive.
- 1 March 2022: New introductory tutorial, including a full walk-through of the new CrystFEL GUI and updated recommendations about data processing.
- 14 January 2022: CrystFEL version 0.10.1 released. This is largely a bug-fixing release, but there are also some interesting new features. Read the release notes for details. See the download page or the changes page for more information.
- 16 August 2021: CrystFEL version 0.10.0 released, featuring the brand new graphical user interface! Here are the release notes with the main points. See the download page or the changes page for more information.
- 25 June 2020: CrystFEL version 0.9.1 released. This is a maintenance and bug-fixing release - here are the release notes with the main points. See the download page or the changes page for more information.
- 6 February 2020: CrystFEL version 0.9.0 released! Here are the release notes with the main points. See the download page or the changes page for more information.
- 4 February 2019: A new article about CrystFEL, providing a step-by-step guide to processing a dataset.
Acknowledgements
The development of CrystFEL is led by Thomas White at the Deutsches Elektronen-Synchrotron DESY in Hamburg, Germany. DESY is a research centre of the Helmholtz Gemeinschaft. See the contact page for more contact details. Prior to 2022, CrystFEL was developed at the Center for Free-Electron Laser Science. Since 2022, its development continues in the Scientific Computing Group of DESY Photon Science.
Code has been contributed to CrystFEL by Valerio Mariani, Helen Ginn, Oleksandr Yefanov, Steve Aplin, Thomas Grant, Mamoru Suzuki, Keitaro Yamashita, Takanori Nakane, Parker de Waal, Wolfgang Brehm, Alexandra Tolstikova, Fedor Chervinskii, Cornelius Gati, Anton Barty, Karol Nass, Nadia Zatsepin, Chun Hong Yoon, Lorenzo Galli, Andrew Martin, Andrew Aquila, Rick Kirian and Ken Beyerlein. The design of CrystFEL and its algorithms has been influenced by Henry Chapman, Petra Fromme, James Holton, John Spence and several others.
Development of CrystFEL is primarily funded by the Helmholtz Association through DESY. Additional funding for CrystFEL has been provided by:
- European Union's Horizon 2020 research and innovation programme under grant agreement No 857641 (ExPaNDS) (2019-2023).
- X-Probe, a project of the European Union's 2020 Research and Innovation Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018).
- The BMBF German-Russian Cooperation SyncFELMed, grant 05K14CHA (2014-2017).
- BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the European Commission.
Useful references
Here are some papers describing CrystFEL or its algorithms:
- T. A. White. "Processing serial crystallography data with CrystFEL: a step-by-step guide". Acta Cryst. D75 (2019).
doi:10.1107/S205979831801238X — Download PDF - T. A. White, V. Mariani, W. Brehm, O. Yefanov, A. Barty, K. R. Beyerlein, F. Chervinskii, L. Galli, C. Gati, T. Nakane, A. Tolstikova, K. Yamashita, C. H. Yoon, K. Diederichs and H. N. Chapman. "Recent developments in CrystFEL". J. Applied Crystallography 49 (2016) p680-689.
doi:10.1107/S1600576716004751 — Download PDF - O. Yefanov, V. Mariani, C. Gati, T. A. White, H. N. Chapman and A. Barty. "Accurate determination of segmented X-ray detector geometry". Optics Express 23 (2015) p28459-28470.
doi:10.1364/OE.23.028459 — Download PDF - T. A. White. "Post-refinement method for snapshot serial crystallography". Phil. Trans. Roy. Soc. B 369 (2014) 20130330.
doi:10.1098/rstb.2013.0330 — Download PDF - T. A. White, A. Barty, F. Stellato, J. M. Holton, R. A. Kirian, N. A. Zatsepin and H. N. Chapman. "Crystallographic data processing for free-electron laser sources". Acta Cryst. D69 (2013), p1231–1240.
doi:10.1107/S0907444913013620 — Download PDF - T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman. "CrystFEL: a software suite for snapshot serial crystallography". J. Appl. Cryst. 45 (2012), p335–341.
doi:10.1107/S0021889812002312 — Download PDF — Article on IUCr website - R. A. Kirian, X. Wang, U. Weierstall, K. E. Schmidt, J. C. H. Spence, M. Hunter, P. Fromme, T. White, H. N. Chapman and J. Holton. "Femtosecond protein nanocrystallography - data analysis methods". Optics Express 18 (2010) p5713. doi:10.1364/OE.18.005713 — Download PDF