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
142
143
144
145
146
147
148
149
150
151
|
.\"
.\" partialator man page
.\"
.\" Copyright © 2012 Thomas White <taw@physics.org>
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"
.TH PARTIALATOR 1
.SH NAME
partialator \- scaling and post-refinement of partial reflections
.SH SYNOPSIS
.PP
.B partialator
\fB-i\fR \fIinput.stream\fR
\fB-o\fR \fIoutput.hkl\fR
\fB-g\fR \fIdetector.geom\fR
\fB-b\fR \fIbeamline.beam\fR
\fB-y\fR \fIpointgroup\fR
[\fBoptions\fR] \fB...\fR
.PP
.B partialator
\fB--help\fR
.SH DESCRIPTION
\fBpartialator\fR merges reflections by scaling and post refinement, accounting
for the partialities of the reflections. That means that it models the geometry
of diffraction for each pattern (crystal orientation, unit cell parameters,
X-ray bandwidth and so on) and attempts to optimise the geometrical parameters
to make the fully integrated intensities calculated using the model agree as
closely as possible between the many patterns.
.PP
This program is \fIexperimental\fR in this version of CrystFEL. It is not yet
considered ready for processing experimental data.
.SH OPTIONS
.PD 0
.IP "\fB-i\fR \fIfilename\fR"
.IP \fB--input=\fR\fIfilename\fR
.PD
Give the name of the input stream..
.PD 0
.IP "\fB-o\fR \fIfilename\fR"
.IP \fB--output=\fR\fIfilename\fR
.PD
Give the name of the output file. The default is
\fB--output=partialator.hkl\fR.
.PD 0
.IP "\fB-y\fR \fIpointgroup\fR"
.IP \fB--symmetry=\fR\fIpointgroup\fR
.PD
Merge according to symmetry \fIpointgroup\fR.
.PD 0
.IP "\fB-g\fR \fIfilename\fR"
.IP \fB--geometry=\fR\fIfilename\fR
.PD
Read the detector geometry description from \fIfilename\fR. See \fBman crystfel_geometry\fR for more information.
.PD 0
.IP "\fB-b\fR \fIfilename\fR"
.IP \fB--beam=\fR\fIfilename\fR
.PD
Read the beam description from \fIfilename\fR. See \fBman crystfel_geometry\fR for more information.
.PD 0
.IP "\fB-n\fR \fIn\fR"
.IP \fB--iterations=\fR\fIn\fR
.PD
Run \fIn\fR cycles of scaling and post refinement.
.PD 0
.IP \fB--no-scale\fR
.PD
Fix all the overall scaling factors to be unity.
.PD 0
.IP "\fB-r\fR \fIfilename\fR"
.IP \fB--reference=\fR\fIfilename\fR
.PD
Refine and scale patterns against the reflections in \fIfilename\fR, instead of
comparing them against each other.
.PD 0
.IP "\fB-m\fR \fImodel\fR"
.IP \fB--model=\fR\fImodel\fR
.PD
Specify the partiality model. See the list below for possible choices.
.PD 0
.IP "\fB-j\fR \fIn\fR"
.PD
Run \fIn\fR analyses in parallel.
.PD 0
.IP \fB--no-polarisation\fR
.PD
Disable the polarisation correction.
.SH PARTIALITY MODELS
The available partiality models are:
.IP \fBsphere\fR
.PD
The volume of intersection between a sphere centered on each reciprocal lattice
point, and the part of reciprocal space excited by the Ewald sphere taking into
account the finite bandwidth and convergence angle. A Lorentz factor will also
be used, proportional to the distance between the limiting Ewald spheres.
For a fully description including diagrams, see T. A. White et al., Acta Cryst.
D69 (2013) p1231-1240.
.IP \fBunity\fR
.PD
Fix all partialities at 1, and use no Lorentz factor at all.
.SH BUGS
This program is \fIexperimental\fR in this version of CrystFEL. It is not
yet considered ready for processing experimental data. Your pet kitten may
explode if you attempt to solve a structure using intensities calculated by this
program.
.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
partialator, 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 indexamajig (1),
.BR process_hkl (1),
.BR partial_sim (1),
.BR crystfel_geometry (5).
|
