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.\"
.\" render_hkl man page
.\"
.\" Copyright © 2012 Thomas White <taw@physics.org>
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"
.TH RENDER_HKL 1
.SH NAME
render_hkl \- render 2D slices of reciprocal space from reflection data
.SH SYNOPSIS
.PP
.B render_hkl [\fIoptions\fR] \fB...\fR \fB-p\fR \fIunitcell.pdb\fR \fIfile.hkl\fR
.PP
\fBrender_hkl --help\fI
.SH DESCRIPTION
render_hkl takes a set of reflection data and plots 2D central sections of the reciprocal lattice as circles using a colour scale in a PDF file. You need to provide, at a minimum, the reflection data and a PDB file with at least a CRYST1 line containing the unit cell parameters.
.SH OPTIONS
.PD 0
.IP \fB-d\fR \fIh,k,l\fR
.IP \fB--down=\fR\fIh,k,l\fR
.PD
Specify the indices for the downward direction of the resulting plot. Default: \fB--down=1,0,0\fR.
.PD 0
.IP \fB-r\fR \fIh,k,l\fR
.IP \fB--right=\fR\fIh,k,l\fR
.PD
Specify the indices for the 'right' direction of the resulting plot. The direction will be approximately to the right, the exact direction depending on the unit cell. Default: \fB--right=0,1,0\fR.
.PD 0
.IP \fB-o\fR \fIfilename\fR
.IP \fB--output=\fR\fIfilename\fR
.PD
Write the output (in PDF format) to \fIfilename\fR. Default: \fB--output=za.pdf\fR.
.PD 0
.IP \fB-p\fR \fIfilename\fR
.IP \fB--pdb=\fR\fIfilenamefR
.PD
Get the unit cell parameters from the CRYST1 line contained in \fIfilename\fR.
.PD 0
.IP \fB--boost=\fR\fIn\fR
.PD
Squash the colour scale by a factor of \fIn\fR. When \fIn\fR=1, the top of the colour scale will represent the highest intensity found in the \fIdata set\fR (not the highest intensity found in the \fIprojection\fR).
.PD 0
.IP \fB-y\fR \fIpointgroup\fR
.IP \fB--symmetry=\fR\fIpointgroup\fR
.PD
Specify the symmetry of the reflection list.
.PD 0
.IP \fB-c\fR \fIscale\fR
.IP \fB--colscale=\fR\fIscale\fR
.PD
Use \fIscale\fR as the colour scale. Possible scales are: \fBmono\fR, \fBinvmono\fR and \fBcolour\fR.
.PD 0
.IP \fB-w\fR \fIweight\fR
.IP \fB--weighting=\fR\fIweight\fR
.PD
Colour the reciprocal lattice points according to \fIweight\fR. Possibilities for \fIweight\fR are:
.RS
.IP \fBI\fR
.PD
The intensities of the reflections
.IP \fBsqrtI\fR
.PD
The square roots of the intensities of the reflections. Negative intensities will be set to zero.
.IP \fBcount\fR
.PD
The numbers of observations of the reflections. The numbers will be corrected for the point group multiplicities of the reflections according to the given symmetry (see \fB--symmetry\fR).
.IP \fBrawcts\fR
.PD
The raw numbers of observations of the reflections, without performing the correction described for \fBcount\fR.
.RE
.PP
The default is \fB--weighting=I\fR.
.PD 0
.IP \fB--colour-key\fR
.PD
Write the selected colour scale out to 'key.pdf' in the current directory.
.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
Copyright © 2012 Thomas White <taw@physics.org>
.P
render_hkl is 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 check_hkl (1)
and
.BR hdfsee (1)
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