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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/).
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 previously been provided by:
* 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 © 2012-2023 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 <http://www.gnu.org/licenses/>.
|
