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author | Thomas White <taw@physics.org> | 2021-03-05 11:10:02 +0100 |
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committer | Thomas White <taw@physics.org> | 2021-03-05 11:10:45 +0100 |
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diff --git a/README.md b/README.md new file mode 100644 index 00000000..8306c030 --- /dev/null +++ b/README.md @@ -0,0 +1,134 @@ +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). + |