1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
|
.\"
.\" render_hkl man page
.\"
.\" Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
.\" a research centre of the Helmholtz Association.
.\"
.\" 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--zone=\fR\fIz\fR
.PD
Show reflections for which \fBg\fR.\fBr\fR=\fIz\fR, where \fBg\fR is the
reflection index (i.e. hkl) and \fBr\fR is the zone axis direction. \fIz\fR
hence represents the Laue zone number.
.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 \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--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--scale-top=\fIn\fR
.PD
Force the top of the colour scale to correspond to a value of \fIn\fR. Any value you give for \fB--boost\fR will be ignored.
.PD 0
.IP \fB--colour-key\fR
.PD
Write the selected colour scale out to 'key.pdf' in the current directory.
.PD 0
.IP \fB--res-ring=\fBres\fR
.PD
Draw a resolution ring at \fIres\fR Angstroms. You can use this option multiple times to get more than one ring.
.PD 0
.IP \fB--highres=\fBres\fR
.PD
Render spots only up to \fIres\fR Angstroms.
.PD 0
.IP \fB--no-axes\fR
.PD
Do not draw the reciprocal space axes on top of the plot.
.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 © 2012-2021 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.P
render_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 hdfsee (1)
|
