CRYSTFEL(7)

NAME
CrystFEL - data processing for serial crystallography

DESCRIPTION
CrystFEL is a suite of programs for processing data from serial crystallography experiments, performed at synchrotron and X-ray free-electron laser facilities, as well as in your home lab using an electron microscope. The programs in the suite are:

indexamajig
    Batch indexing, integration and data reduction program, which produces a "stream" containing the indexing and integration results for each diffraction pattern.

process_hkl
    A tool merging intensities from many patterns into a single reflection list, via the Monte Carlo method.

partialator
    Full scaling and post-refinement process for accurate merging of data and outlier rejection.

ambigator
    A tool for resolving indexing ambiguities.

get_hkl
    A tool for manipulating reflection lists, such as performing symmetry expansion.

cell_tool
    A tool for manipulating unit cell files, such as applying transformations.

cell_explorer
    A tool for examining the distributions of unit cell parameters.

compare_hkl and check_hkl
    Tools for calculating figures of merit, such as completeness and R-factors.

render_hkl
    A tool for rendering slices of reciprocal space in two dimensions.

align_detector
    A program to refine and optimize detector geometry.

list_events
    A tool for creating lists of events from multi-event data files.

whirligig
    A tool for locating runs of crystals with similar orientations, e.g. from 'mini rotation series' arising from the use of a slow extrusion sample injector.

make_pixelmap
    A tool for creating pixel maps for Cheetah, OnDA etc.

adjust_detector
    A tool to alter detector geometry.

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.

Please see the individual manual pages for the CrystFEL programs for detailed information.

CITING CRYSTFEL
If CrystFEL was important for your research, please consider citing the following article:

    T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman. "CrystFEL: a software suite for snapshot serial crystallography". J. Appl. Cryst. 45. doi:10.1107/S0021889812002312

Please let us know (see below) about your publication, so we can include it in the list of examples on the CrystFEL website.

SYMMETRY IN CRYSTFEL
Without only a very few exceptions, CrystFEL is not interested in space groups. Instead, it deals with point groups which embody the information about how data should be merged from different crystals. Every space group belongs to exactly one point group, and you can look up the right one in the International Tables or using the symmetry tables accompanying the CrystFEL source (or to be found on the CrystFEL website in the Theory section). You can append _uaX to any of the point group symbols listed below, where X is a, b or c. This will specify the 'unique' axis for lattices which have one. The default unique axis, where this makes sense, is c. Here is a list of all the possible crystallographic point groups, written as they will be accepted by CrystFEL. Refer to this list if you experience difficulty with "-y" at any time.

Triclinic
    1, -1.

Monoclinic
    2/m, 2, m.

Orthorhombic
    mmm, 222, mm2.

Tetragonal
    4/m, 4, -4, 4/mmm, 422, -42m, -4m2, 4mm.

Trigonal (rhombohedral axes)
    3_R, -3_R, 32_R, 3m_R, -3m_R.

Trigonal (hexagonal axes)
    3_H, -3_H, 321_H, 312_H, 3m1_H, 31m_H, -3m1_H, -31m_H.

Hexagonal
    6/m, 6, -6, 6/mmm, 622, -62m, -6m2, 6mm.

Cubic
    23, m-3, 432, -43m, m-3m.

FUNDING ACKNOWLEDGEMENTS
Development of CrystFEL is primarily funded by the Helmholtz Association via DESY. Partial funding for CrystFEL has been provided by: * The consortium DAPHNE4NFDI in the context of the work of the NFDI e.V. The
  consortium is funded by the Deutsche Forschungsgemeinschaft (DFG, German
  Research Foundation) - project number 460248799 (2022-). * European Union’s Horizon 2020 research and innovation programme under grant
  agreement No 857641 (ExPaNDS) (2019-2023). * 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).

AUTHOR
This page was written by Thomas White and Valerio Mariani.

REPORTING BUGS
Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.

COPYRIGHT AND DISCLAIMER
Copyright © 2012-2024 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.

Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and 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/>.

SEE ALSO
indexamajig(1), process_hkl(1), partialator(1), compare_hkl(1), check_hkl(1), render_hkl(1), get_hkl(1), cell_tool(1), whirligig(1), list_events(1), make_pixelmap(1), crystfel_geometry(5).