CrystFEL - Data processing for serial crystallography ===================================================== Overview -------- CrystFEL is a suite of programs for processing data from [serial crystallography experiments](https://en.wikipedia.org/wiki/Serial_Femtosecond_Crystallography), performed at synchrotron and X-ray free-electron laser facilities, as well as in your home lab using an electron microscope. Getting started --------------- See [INSTALL.md](INSTALL.md) for installation instructions, including our container registry, installation via package manager and details of pre-existing installations at X-ray facilities around the world. CrystFEL can be used from the command line or via a graphical user interface. To start the graphical user interface, run ```crystfel```. There is a [video tutorial](https://vimeo.com/585412404), as well as a [text tutorial](doc/articles/tutorial.rst) to get you started with processing via the GUI. For command-line use, standard ```man``` pages are available. Start with ```man crystfel```. The manual pages are also [available on the web](https://www.desy.de/~twhite/crystfel/manual.html). Documentation ------------- * [Basic Tutorial](doc/articles/tutorial.rst) * [How to choose the right point group for merging](doc/articles/pointgroup.rst) * [How to increase data processing speed](doc/articles/speed.rst) * [Real-time data processing](doc/articles/online.rst) * [Processing electron diffraction data](doc/articles/electrons.rst) * [Symmetry classification for serial crystallography](doc/twin-calculator.pdf) * [Matrix conventions used in CrystFEL code](doc/matrix-notation.pdf) - for developers, written mostly for my own benefit. * [Hit rate graph](doc/hitrate.png) * [Examples folder](doc/examples) - contains some template input files. * [Contributing to CrystFEL](CONTRIBUTING.md) - including how to cite CrystFEL and how to find good first issues to work on. * [Citation list](https://www.desy.de/~twhite/crystfel/citations.html) - please send us details of your paper, if it's missing! * [Scripts folder](scripts) - a miscellany of smaller programs to help at various stages of data processing. Journal articles and book chapters ---------------------------------- * [Processing serial crystallography data with CrystFEL: a step-by-step guide](https://doi.org/10.1107/S205979831801238X) - covers command-line processing only (pre-dates the GUI). * [Recent developments in CrystFEL](http://dx.doi.org/10.1107/S1600576716004751) - now somewhat out of date, but contains some useful information about the algorithms used. * [Crystallography and Molecular Imaging using X-ray Lasers](https://doi.org/10.23730/CYRSP-2018-001.605) - an introduction to the biological aspects and possibilities, written for physicists (in contrast to most other articles, which introduce the physical aspects for biologists!). * [Original paper about CrystFEL](http://dx.doi.org/10.1107/S0021889812002312) from 2012. Not open access, but a "reprint" is available [here](https://www.desy.de/~twhite/crystfel/db5097-reprint.pdf). * [Climbing the Data Mountain: Processing of SFX Data](https://link.springer.com/chapter/10.1007/978-3-030-00551-1_7) - emphasizes data volume issues for XFELs. Unfortunately not open access. * [Processing of XFEL Data](https://link.springer.com/protocol/10.1007/978-1-4939-7000-1_13) - describes the entire processing pipeline. Unfortunately not open access. Awards ------ In 2017, the development of CrystFEL was recognised with the [Max von Laue Prize](https://www.desy.de/news/news_search/index_eng.html?openDirectAnchor=1202) from the [German Society for Crystallography (DGK)](https://dgk-home.de/en/). Citing CrystFEL --------------- Please see [CONTRIBUTING.md](CONTRIBUTING.md) for citation instructions. Funding acknowledgements ------------------------ Development of CrystFEL is primarily funded by the [Helmholtz Association](https://www.helmholtz.de/) via [DESY](https://www.desy.de/). Partial funding for CrystFEL has been provided by: * The consortium DAPHNE4NFDI in the context of the work of the NFDI e.V. The consortium is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project number 460248799 (2022-). * European Union’s Horizon 2020 research and innovation programme under grant agreement No 857641 ([ExPaNDS](https://expands.eu/)) (2019-2023). * [X-Probe](http://x-probe.org/), a project of the European Union's 2020 Research and Innovation Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018). * The [BMBF](https://www.bmbf.de/) German-Russian Cooperation [SyncFELMed](http://www.syncfelmed.org/), grant 05K14CHA (2014-2017). * [BioStruct-X](https://www.biostruct-x.eu/), a project funded by the Seventh Framework Programme (FP7) of the European Commission (2011-2016). Licence ------- Copyright © 2012-2024 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. See [AUTHORS](AUTHORS) as well as individual source code files for full details of contributors. CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with CrystFEL. If not, see .