From f454fe20ccb3e1b93f88b93ab35cd8465140d900 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 2 Mar 2012 10:53:31 +0100 Subject: Manual page for render_hkl --- doc/man/render_hkl.1 | 98 ++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 96 insertions(+), 2 deletions(-) (limited to 'doc/man') diff --git a/doc/man/render_hkl.1 b/doc/man/render_hkl.1 index 2b206ece..3e1408e9 100644 --- a/doc/man/render_hkl.1 +++ b/doc/man/render_hkl.1 @@ -11,7 +11,101 @@ render_hkl \- render 2D slices of reciprocal space from reflection data .SH SYNOPSIS .PP -.B render_hkl -[options] +.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 , or visit . + +.SH COPYRIGHT +Copyright © 2012 Thomas White +.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 . + +.SH SEE ALSO +.BR check_hkl (1) +and +.BR hdfsee (1) -- cgit v1.2.3