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.\"
.\" compare_hkl man page
.\"
.\" Copyright © 2012 Thomas White <taw@physics.org>
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"
.TH COMPARE_HKL 1
.SH NAME
compare_hkl \- compare reflection data
.SH SYNOPSIS
.PP
\fBcompare_hkl\fR \fR [\fIoptions\fR] \fB...\fR \fIfile1.hkl\fR \fIfile2.hkl\fR
.PP
\fBcompare_hkl --help\fR
.SH DESCRIPTION
compare_hkl compares two sets of reflection data and calculates figures of merit such as R-factors. Reflections will be considered equivalent according to your choice of point group.
.SH OPTIONS
.PD 0
.IP \fB-y\fR \fpointgroup\fR
.IP \fB--symmetry=\fR\fIpointgroup\fR
.PD
Specify the symmetry of the reflections. The symmetry must be the same for both lists of reflections. Default: 1 (no symmetry).
.PD 0
.IP \fB-p\fR \fIunitcell.pdb\fR
.IP \fB--pdb=\fR\fIunitcell.pdb\fR
.PD
Specify the name of the PDB file containing at least a CRYST1 line describing the unit cell.
.PD 0
.IP \fB--fom=\fR\fIFoM\fR
.PD
Calculate figure of merit \fIFoM\fR. Possible figures of merit are:
.RS
.IP \fBRsplit\fR
.PD
2^(-0.5) * sum(I1-kI2) / [ 0.5*sum(I1+kI2) ]
.IP \fBR1f\fR
.PD
sum(sqrt(I1)-sqrt(kI2)) / sum(sqrt(I1))
.IP \fBR1i\fR
.PD
sum(I1-kI2) / sum(I1)
.IP \fBR2\fR
.PD
sqrt(sum[(I1-kI2)^2] / sum(I1^2))
.IP \fBCC\fR
.PD
The Pearson correlation coefficient.
.IP \fBCC*\fR
.PD
See Karplus and Diederichs, Science 336 (2012) p1030.
.PP
I1 and I2 are the intensities of the same reflection in both reflection lists. The scale factor, k, is given by sum(I1*i2) / sum(I2^2), unless you use \fB-u\fR.
.RE
.PD 0
.IP \fB-u\fR
.PD
Fix scale factors to unity.
.PD 0
.IP \fB--nshells=\fR\fIn\fR
.PD
Use \fIn\fR resolution shells. Default: 10.
.PD 0
.IP \fB--shell-file=\fIfilename\fR
.PD
Write the figure of merit in resolution shells to \fIfilename\fR. Default: "shells.dat".
.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--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
Discard reflections with lower than this value of 1/d in m^-1.
.PD 0
.IP \fB--rmax=\fR\fI1/d\fR
.PD
Discard reflections with higher than this value of 1/d in m^-1.
.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 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.P
compare_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),
.BR check_hkl (1),
.BR render_hkl (1)
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