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CrystFEL - Crystallography with a FEL
-------------------------------------
Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
a research centre of the Helmholtz Association.
Authors:
Thomas White <taw@physics.org>
Richard Kirian <rkirian@asu.edu>
Kenneth Beyerlein <kenneth.beyerlein@desy.de>
Andrew Aquila <andrew.aquila@cfel.de>
Andrew Martin <andrew.martin@desy.de>
Lorenzo Galli <lorenzo.galli@desy.de>
Chun Hong Yoon <chun.hong.yoon@desy.de>
Kenneth Beyerlein <kenneth.beyerlein@desy.de>
Karol Nass <karol.nass@desy.de>
Nadia Zatsepin <nadia.zatsepin@asu.edu>
Anton Barty <anton.barty@desy.de>
Cornelius Gati <cornelius.gati@desy.de>
Fedor Chervinskii <fedor.chervinskii@gmail.com>
Alexandra Tolstikova <alexandra.tolstikova@desy.de>
Wolfgang Brehm <wolfgang.brehm@gmail.com>
Valerio Mariani <valerio.mariani@desy.de>
Parker de Waal <Parker.deWaal@vai.org>
Takanori Nakane <nakane.t@gmail.com>
Keitaro Yamashita <k.yamashita@spring8.or.jp>
Marmoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp>
Thomas Grant <tgrant@hwi.buffalo.edu>
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/>.
Thank you for reading the documentation. :-)
CrystFEL is a suite of programs for processing (and simulating) Bragg
diffraction data acquired with a 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. Unique correction factors are
needed.
- The crystals are small, leading to significant Fourier truncation effects on
the detector.
- Many patterns (>10,000) 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
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
------------
See the "INSTALL" file for the generic instructions on how to use the build
system. In short, it's the usual:
$ ./configure
$ make
$ make check
$ sudo make install
If you have libraries installed in strange places, you might want to do
something similar to one of these instead of the first step:
$ ./configure --with-opencl
$ ./configure --with-hdf5=/some/strange/location
$ ./configure --with-libtiff=/some/strange/location
$ ./configure --with-gsl=/some/strange/location
$ ./configure --disable-gtk
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 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 you're compiling on Mac OS X, where GTK, libPNG and libTIFF seem to be much
harder to come by, disable lots of things:
$ ./configure --disable-gtk --disable-png --disable-libtiff
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.
If you get an error about "cairo_surface_show_page" in src/scaling-report.c,
simply edit the file and comment that line out. Partialator will then not be
able to produce a useful scaling report, but the rest of CrystFEL will work
properly.
If you are installing from Git, the following extra things apply:
- You must run "./autogen.sh" to generate "configure" and other files before
proceeding as detailed above.
- If you have an old version of Automake (less than 1.10), or an old version of
Autoconf (less than 2.60), you'll need to add the following line near the top
of Makefile.am:
docdir = ${datadir}/doc/${PACKAGE}
- If your Automake version is less than 1.11, you'll need to comment out the
reference to AM_SILENT_RULES in configure.ac, like this:
dnl AM_SILENT_RULES([yes])
- You will not be able to use the "--enable-gtk-doc" option to configure unless
you have at least version 1.9 of gtk-doc installed.
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.
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