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authorThomas White <taw@physics.org>2021-03-05 11:10:02 +0100
committerThomas White <taw@physics.org>2021-03-05 11:10:45 +0100
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+CrystFEL - Data processing for serial crystallography
+=====================================================
+
+Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
+ a research centre of the Helmholtz Association.
+
+See AUTHORS for full details of contributors.
+
+Introduction
+------------
+
+CrystFEL is a suite of programs for processing (and simulating) Bragg
+diffraction data from "serial crystallography" experiments, often (but not
+always) performed using an X-ray Free-Electron Laser. Compared to rotation data,
+some of the particular characteristics of such data which call for a
+specialised software suite are:
+
+* The sliced, rather than integrated, measurement of intensity data. Many, if
+ not all reflections are partially integrated.
+
+* Many patterns (thousands) are required - high throughput is needed.
+
+* The crystal orientations in each pattern are random and uncorrelated.
+
+* Merging into lower symmetry point groups may require the resolution of
+ indexing ambiguities.
+
+
+Getting started
+---------------
+
+The best way to get started, after installation, is to run command ```crystfel```
+to start the graphical user interface.
+
+
+Installation
+------------
+
+CrystFEL installation is supported on GNU/Linux and Mac OS X. The terse
+installation instructions below should be enough if you're experienced with
+installing software from source. More detailed installation information is
+available [on the website](https://www.desy.de/~twhite/crystfel/install.html).
+
+Here are the mandatory dependencies - you cannot install CrystFEL without these:
+
+* Either [CMake](https://cmake.org/) 3.12 or later or [Meson](https://mesonbuild.com/) (Meson is preferred)
+* [HDF5](https://www.hdfgroup.org/downloads/hdf5/) 1.8.0 or later (1.10.0 or later is required for many recent data formats)
+* [GNU Scientific Library (GSL)](https://www.gnu.org/software/gsl/)
+* [Bison](https://www.gnu.org/software/bison/) 2.6 or later
+* [Flex](https://www.gnu.org/software/flex/)
+* [Zlib](https://www.zlib.net/) (1.2.3.5 or later preferred for better decompression speed)
+
+The following dependencies are "optional", in the sense that you can install
+CrystFEL without them. However, a CrystFEL installation without these will lack
+important features such as the graphical user interface:
+
+* GTK3 or later
+* Cairo
+* Pango
+* gdk-pixbuf
+* NCurses
+* libPNG
+* [libccp4](ftp://ftp.ccp4.ac.uk/opensource/)
+
+Note that all of the dependencies mentioned above (including libccp4) should be
+available from your Linux distribution's package manager, or from
+[Homebrew](https://brew.sh/) on Mac OS. You should not need to download and
+install any of them separately from source, and we emphatically recommend
+against trying to do so!
+
+Note that using the libraries from the full CCP4 suite is not recommended. CCP4
+includes so many other libraries that it becomes very difficult to link using
+the correct versions of everything.
+
+Processing data relies on indexing algorithms. The more of the following are
+installed, the better your experience will be:
+
+* [FFTW3](http://fftw.org/)
+* [XGandalf](https://stash.desy.de/users/gevorkov/repos/xgandalf)
+* [PinkIndexer](https://stash.desy.de/users/gevorkov/repos/pinkindexer)
+* [Mosflm](https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/)
+* [DirAx](http://www.crystal.chem.uu.nl/distr/dirax/)
+* [XDS](http://xds.mpimf-heidelberg.mpg.de/)
+
+Installation follows the normal CMake procedure:
+
+```
+$ mkdir build
+$ cd build
+$ cmake ..
+$ make
+$ sudo make install
+```
+
+Or, with Meson:
+
+```
+$ meson . build
+$ ninja -C build
+$ sudo ninja -C build install
+```
+
+
+Licence
+-------
+
+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/>.
+
+
+Funding acknowledgements
+------------------------
+
+Development of CrystFEL is primarily funded by the Helmholtz Association.
+
+Partial funding for CrystFEL has previously been provided by:
+
+- "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 (2011-2016).
+