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.\"
.\" CrystFEL main man page
.\"
.\" Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
.\" a research centre of the Helmholtz Association.
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"
.TH CRYSTFEL 7
.SH NAME
CrystFEL \- data processing for FEL crystallography
.SH DESCRIPTION
CrystFEL is a suite of programs for processing Bragg diffraction data acquired with a free electron laser in a "serial" manner. Some of the particular characteristics of such data which call for a specialised software suite are:
.RS
Each crystal is used for only one exposure, and there is no oscillation, rotation nor a large bandwidth or divergence. Therefore, many or all reflections are partially integrated.
.PP
The crystals might be very small and the illumination highly coherent, leading to significant Fourier truncation effects on the detector.
.PP
Many patterns, numbering tens of thousands or more, are required, so high throughput automated processing is important.
.PP
The crystal orientations in each pattern are random and uncorrelated, which leads to special considerations during scaling and merging.
.RE
CrystFEL includes programs for simulating and processing patterns subject to the
above characteristics. Fifteen programs form the core of CrystFEL. They are:
.IP \fBindexamajig\fR
Batch indexing, integration and data reduction program, which produces a "stream" containing the indexing and integration results for each diffraction pattern.
.IP \fBpattern_sim\fR
A diffraction pattern simulation tool.
.IP \fBprocess_hkl\fR
A tool merging intensities from many patterns into a single reflection list, via the Monte Carlo method.
.IP \fBpartialator\fR
Full scaling and post-refinement process for accurate merging of data and outlier rejection.
.IP \fBambigator\fR
A tool for resolving indexing ambiguities.
.IP \fBget_hkl\fR
A tool for manipulating reflection lists, such as performing symmetry expansion.
.IP \fBcell_explorer\fR
A tool for examining the distributions of unit cell parameters.
.IP "\fBcompare_hkl\fR and \fBcheck_hkl\fR"
Tools for calculating figures of merit, such as completeness and R-factors.
.IP \fBpartial_sim\fB
A tool for calculating partial reflection intensities, perhaps for testing the convergence of Monte Carlo merging.
.IP \fBhdfsee\fR
A simple viewer for images stored in HDF5 format.
.IP \fBrender_hkl\fR
A tool for rendering slices of reciprocal space in two dimensions.
.IP \fBgeoptimiser\fR
A program to refine and optimize detector geometry.
.IP \fBlist_events\fR
A tool for creating lists of events from multi-event data files.
.IP \fBwhirligig\fR
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.
.IP \fBmake_pixelmap\fR
A tool for for creating pixel maps for Cheetah, OnDA etc.
.PP
There is also a folder full of scripts for achieving many related tasks.
.PP
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.
.PP
Please see the individual manual pages for the CrystFEL programs for detailed information.
.SH CITING CRYSTFEL
If CrystFEL was important for your research, please consider citing the
following article:
.IP
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
.PP
Please let us know (see below) about your publication, so we can include it in
the list of examples on the CrystFEL website.
.SH 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 \fB_ua\fR\fIX\fR to any of the point group symbols listed below, where \fIX\fR is \fBa\fR, \fBb\fR or \fBc\fR. This will specify the 'unique' axis for lattices which have one.
\fBThe default unique axis, where this makes sense, is c\fR.
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.
.IP Triclinic
\fB1\fR, \fB-1\fR.
.IP Monoclinic
\fB2/m\fR, \fB2\fR, \fBm\fR.
.IP Orthorhombic
\fBmmm\fR, \fB222\fR, \fBmm2\fR.
.IP Tetragonal
\fB4/m\fR, \fB4\fR, \fB-4\fR, \fB4/mmm\fR, \fB422\fR, \fB-42m\fR, \fB-4m2\fR, \fB4mm\fR.
.IP "Trigonal (rhombohedral axes)"
\fB3_R\fR, \fB-3_R\fR, \fB32_R\fR, \fB3m_R\fR, \fB-3m_R\fR.
.IP "Trigonal (hexagonal axes)"
\fB3_H\fR, \fB-3_H\fR, \fB321_H\fR, \fB312_H\fR, \fB3m1_H\fR, \fB31m_H\fR, \fB-3m1_H\fR, \fB-31m_H\fR.
.IP Hexagonal
\fB6/m\fR, \fB6\fR, \fB-6\fR, \fB6/mmm\fR, \fB622\fR, \fB-62m\fR, \fB-6m2\fR, \fB6mm\fR.
.IP Cubic
\fB23\fR, \fBm-3\fR, \fB432\fR, \fB-43m\fR, \fBm-3m\fR.
.SH 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.
.SH AUTHOR
This page was written by Thomas White and Valerio Mariani.
.SH REPORTING BUGS
Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
.SH COPYRIGHT AND DISCLAIMER
.PD 0
Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.PD
.PP
Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors.
.P
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.
.P
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.
.P
You should have received a copy of the GNU General Public License along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
.SH SEE ALSO
.BR indexamajig (1),
.BR process_hkl (1),
.BR partialator (1),
.BR pattern_sim (1),
.BR partial_sim (1),
.BR compare_hkl (1),
.BR check_hkl (1),
.BR render_hkl (1),
.BR hdfsee (1),
.BR get_hkl (1),
.BR geoptimiser (1),
.BR whirligig (1),
.BR list_events (1),
.BR make_pixelmap (1),
.BR crystfel_geometry (5).
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