CrystFEL - Crystallography with a FEL ------------------------------------- Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. Authors: Thomas White Richard Kirian Kenneth Beyerlein Andrew Aquila Andrew Martin Lorenzo Galli Chun Hong Yoon Kenneth Beyerlein Karol Nass Nadia Zatsepin Anton Barty Cornelius Gati Fedor Chervinskii Alexandra Tolstikova Wolfgang Brehm Valerio Mariani Parker de Waal Takanori Nakane Keitaro Yamashita Mamoru Suzuki Thomas Grant Steve Aplin Oleksandr Yefanov Helen Ginn Nicolas Riebesel Yaroslav Gevorkov Omri Mor 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 . Thank you for reading the documentation. :-) 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. 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, meaning that: - Merging into lower symmetry point groups may require the resolution of indexing ambiguities. CrystFEL includes programs for simulating and processing patterns subject to the above characteristics. The main programs are: - indexamajig, a "batch indexer" and data reduction program. - process_hkl, for merging per-pattern lists of intensities into a single reflection list. - cell_explorer, for examining distributions of lattice parameters. - ambigator, a tool for resolving indexing ambiguities, - geoptimiser, for refining detector geometry. - whirligig, for finding multiple shots from single crystals. - partialator, for merging patterns more accurately (and much more slowly) using post refinement. In addition, there is also: - get_hkl, for doing various simple operations on reflection lists. - compare_hkl, for working out the differences (e.g. a q-dependent scaling factor) between two lists of reflections. - check_hkl, for determining things like completeness. - pattern_sim, for simulating patterns. - partial_sim, for calculating partial reflection intensities. - hdfsee, a simple viewer for images stored in HDF5 format. - render_hkl, for turning reflection lists into pretty graphics. - list_events, for creating event lists from multi-event files. - make_pixelmap, for creating pixel maps for Cheetah, OnDA etc. There is also a folder full of scripts for achieving many related tasks. CrystFEL mostly works with images stored in HDF5 format, unit cell data in PDB format, and reflection lists in plain text format (i.e. not MTZ). There are scripts for converting both ways between plain text reflection lists and MTZ files. Standard "man" pages are provided for documentation, or you can invoke any program with the argument "--help" to get a summary of options. There are some example geometry and beam description files in doc/examples, and development documentation created using GTK-Doc. Installation ------------ $ mkdir build $ cd build $ cmake .. $ make $ sudo make install At a minimum, you will need the HDF5 library (version 1.8.0 or later) and the GNU Scientific Library (GSL). For a full installation, you will also need libTIFF, libPNG, Cairo, FFTW3, CBFLib and GTK2. All of these should be installed from your distribution's package manager. Be sure to install the development files for each package, which will have a name like "gtk+-2.0-dev" or "gtk+-2.0-devel", depending on which distribution you use. If external libraries have been installed in non-standard locations, you can set the path like this, for example for Xgandalf: cmake -DXGANDALF_INCLUDES=/path/to/xgandalf/include \ -DXGANDALF_LIBRARIES=/path/to/xgandalf/lib/libxgandalf.so The path to HDF5 can be set similarly: cmake -DHDF5_ROOT=/path/to/hdf5 (... /include, /lib etc) Or for CBF, use one of: -DCBF_CBF_INCLUDES=/path/to/cbflib/include (... /cbf/cbf.h) -DCBFLIB_CBF_INCLUDES=/path/to/cbflib/include (... /cbflib/cbf.h) and: -DCBF_LIBRARIES=/path/to/libcbf.so To install CrystFEL in a custom location, use: -DCMAKE_INSTALL_PREFIX=/path/for/crystfel/installation If you get an error mentioning fftw3 and telling you to recompile with -fPIC, then your version of FFTW3 is not compiled in a suitable way. You'll need to install it again (from source) adding "--enable-shared" to its ./configure command line. Funding acknowledgements ------------------------ Development of CrystFEL is primarily funded by the Helmholtz Association via programme-oriented funds. Additional funding for CrystFEL is 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). Additional funding for CrystFEL is provided by the BMBF German-Russian Cooperation "SyncFELMed", grant 05K14CHA (2014-2017). Past funding for CrystFEL has been received from BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the European Commission.