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.\"
.\" CrystFEL main man page
.\"
.\" Copyright © 2012 Thomas White <taw@physics.org>
.\"
.\" 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 import.
.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. Four 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.
.PP
In addition, there is also:
.IP \fBget_hkl\fR
A tool for manipulating reflection lists, such as performing symmetry expansion.
.IP \fBpowder_plot\fR
A tool for the calculation of one-dimensional "powder" traces.
.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.
.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 AUTHOR
This page was written by Thomas White.
.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 Thomas White <taw@physics.org>
.LP
Copyright © 2012 Richard Kirian <rkirian@asu.edu>
.LP
Copyright © 2012 Andrew Aquila <andrew.aquila@cfel.de>
.LP
Copyright © 2012 Andrew Martin <andrew.martin@desy.de>
.LP
Copyright © 2012 Lorenzo Galli <lorenzo.galli@desy.de>
.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 powder_plot (1),
.BR hdfsee (1),
.BR get_hkl (1),
.BR crystfel_geometry (1).
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