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.\"
.\" check_hkl man page
.\"
.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
.\" a research centre of the Helmholtz Association.
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"
.TH CHECK_HKL 1
.SH NAME
check_hkl \- calculate figures of merit for reflection data
.SH SYNOPSIS
.PP
\fBcheck_hkl\fR [\fIoptions\fR] \fB...\fR \fIfile.hkl\fR \fB-p\fR \fIcell.pdb\fR
.PP
\fBcheck_hkl --help\fR
.SH DESCRIPTION
check_hkl calculates figures of merit for reflection data, such as completeness and average signal strengths, in resolution shells. check_hkl accepts a single reflection list in CrystFEL's format, and you must also provide a unit cell (in a PDB file or CrystFEL unit cell format).
.SH OPTIONS
.PD 0
.IP "\fB-p\fR \fIunitcell.cell\fR"
.IP "\fB-p\fR \fIunitcell.pdb\fR"
.IP \fB--pdb=\fR\fIunitcell.pdb\fR
.PD
Specify the name of the file containing unit cell information, in PDB or CrystFEL format.
.PD 0
.IP "\fB-y\fR \fIpointgroup\fR"
.IP \fB--symmetry=\fR\fIpointgroup\fR
.PD
Specify the symmetry of the reflections.
.PD 0
.IP "\fB--sigma-cutoff=\fR\fIn\fR"
.PD
Discard reflections with I/sigma(I) < \fIn\fR. Default: -infinity (no cutoff).
.PD 0
.IP "\fB--rmin=\fR\fI1/d\fR"
.PD
Low resolution cutoff, as 1/d in m^-1. Use this or \fB--lowres\fR, but not both.
.PD 0
.IP "\fB--lowres=\fR\fId\fR"
Low resolution cutoff in Angstroms. Use this or \fB--rmin\fR, but not both.
.PD 0
.IP "\fB--rmax=\fR\fI1/d\fR"
.PD
High resolution cutoff, as 1/d in m^-1. Use this or \fB--highres\fR, but not both.
.PD 0
.IP "\fB--highres=\fR\fId\fR"
High resolution cutoff in Angstroms. Use this or \fB--rmax\fR, but not both.
.PD 0
.IP \fB--shell-file=\fR\fIfilename\fR
.PD
Write the statistics in resolution shells to \fIfilename\fR.
.PD 0
.IP \fB--ltest\fR
.PD
Perform an L-test for twinning. The shell file will contain the values of |L|, N(|L|) and the theoretical values for untwinned and perfectly twinned data. See Padilla and Yeates, Acta Cryst. D59 (2003) p1124.
.PD 0
.IP \fB--wilson\fR
.PD
Calculate a Wilson plot. The shell file will contain the values of s^2 and ln(<I>/eE) (and also the shell number and d in Angstroms for your convenience). The B factor will be calculated using data above 3.2 A resolution and displayed on the terminal.
.IP
Note that the atoms/species in the unit cell need to be known in order to calculate a Wilson plot. The average stoichiometry of protein will be used by check_hkl. This means that the results will be inaccurate for non-protein samples.
.PD 0
.IP \fB--ignore-negs\fR
.PD
Ignore reflections with negative intensities.
.PD 0
.IP \fB--zero-negs\fR
.PD
Set to zero the intensities of reflections with negative intensities.
.PD 0
.IP \fB--nshells=\fIn\fR
.PD
Use \fIn\fR resolution shells. Default: 10.
.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
Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.P
check_hkl, and this manual, are part of CrystFEL.
.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 crystfel (7)
and
.BR compare_hkl (1)
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