Repository navigation
Expand file tree
/
Copy pathquick_start.html
More file actions
149 lines (112 loc) · 6.86 KB
/
Copy pathquick_start.html
File metadata and controls
149 lines (112 loc) · 6.86 KB
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
<!DOCTYPE html>
<html lang="en" data-content_root="./">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Quick start guide — xia2 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
<link rel="stylesheet" type="text/css" href="_static/basic.css?v=b08954a9" />
<link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=27fed22d" />
<link rel="stylesheet" href="_static/xia2.css" type="text/css" />
<script src="_static/documentation_options.js?v=5929fcd5"></script>
<script src="_static/doctools.js?v=fd6eb6e6"></script>
<script src="_static/sphinx_highlight.js?v=6ffebe34"></script>
<script defer="defer" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Using xia2" href="using_xia2.html" />
<link rel="prev" title="Introduction" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
</head><body>
<!-- <div class="logoheader container"> -->
<!-- <a href="index.html"> -->
<!-- <img class="logoheader" alt="DIALS" src="_static/dials_header.png" /> -->
<!-- </a> -->
<!-- </div> -->
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<section id="quick-start-guide">
<h1>Quick start guide<a class="headerlink" href="#quick-start-guide" title="Link to this heading">¶</a></h1>
<p>If you don’t like reading manuals and just want to get started, try:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">xia2</span> <span class="n">pipeline</span><span class="o">=</span><span class="n">dials</span> <span class="o">/</span><span class="n">here</span><span class="o">/</span><span class="n">are</span><span class="o">/</span><span class="n">my</span><span class="o">/</span><span class="n">images</span>
</pre></div>
</div>
<p>or:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">xia2</span> <span class="n">pipeline</span><span class="o">=</span><span class="mi">3</span><span class="n">d</span> <span class="o">/</span><span class="n">here</span><span class="o">/</span><span class="n">are</span><span class="o">/</span><span class="n">my</span><span class="o">/</span><span class="n">images</span>
</pre></div>
</div>
<p>(remembering of course atom=X if you want anomalous pairs separating
in scaling.) If this appears to do something sensible then you may well be
home and dry. Some critical options:</p>
<blockquote>
<div><table class="docutils align-default">
<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Usage</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>atom= X</p></td>
<td><p>tell xia2 to separate anomalous pairs i.e. I(+) <span class="math notranslate nohighlight">\(\neq\)</span> I(−) in scaling</p></td>
</tr>
<tr class="row-odd"><td><p>pipeline=dials</p></td>
<td><p>tell xia2 to use <a class="reference external" href="http://dials.github.io/">DIALS</a></p></td>
</tr>
<tr class="row-even"><td><p>pipeline=dials-aimless</p></td>
<td><p>tell xia2 to use <a class="reference external" href="http://dials.github.io/">DIALS</a> and <a class="reference external" href="http://www.ccp4.ac.uk/html/aimless.html">Aimless</a></p></td>
</tr>
<tr class="row-odd"><td><p>pipeline=3d</p></td>
<td><p>tell xia2 to use <a class="reference external" href="http://xds.mpimf-heidelberg.mpg.de/">XDS</a> and <a class="reference external" href="http://xds.mpimf-heidelberg.mpg.de/html_doc/xscale_program.html">XSCALE</a></p></td>
</tr>
<tr class="row-even"><td><p>pipeline=3dii</p></td>
<td><p>tell xia2 to use <a class="reference external" href="http://xds.mpimf-heidelberg.mpg.de/">XDS</a> and <a class="reference external" href="http://xds.mpimf-heidelberg.mpg.de/html_doc/xscale_program.html">XSCALE</a>, indexing with peaks found from all images</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
<p>If this doesn’t hit the spot, you’ll need to read the rest of the documentation.</p>
</section>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<p class="logo">
<a href="index.html">
<img class="logo" src="_static/xia2-new-logo.gif" alt="Logo" />
</a>
</p>
<h3>Navigation</h3>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Getting started</a></li>
<li class="toctree-l1"><a class="reference internal" href="using_xia2.html">Using xia2</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="introductory_example.html">Introductory example</a></li>
<li class="toctree-l1"><a class="reference internal" href="insulin_tutorial.html">Insulin tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="multi_crystal.html">Multi-crystal data</a></li>
<li class="toctree-l1"><a class="reference internal" href="multiplex/index.html">Multi-crystal data reduction (xia2.multiplex)</a></li>
<li class="toctree-l1"><a class="reference internal" href="serial_crystallography.html">Serial-crystallography</a></li>
<li class="toctree-l1"><a class="reference internal" href="program_output.html">Program output</a></li>
<li class="toctree-l1"><a class="reference internal" href="parameters.html">Parameters</a></li>
<li class="toctree-l1"><a class="reference internal" href="comments.html">Comments</a></li>
<li class="toctree-l1"><a class="reference internal" href="background.html">History</a></li>
<li class="toctree-l1"><a class="reference internal" href="acknowledgements.html">Acknowledgements</a></li>
<li class="toctree-l1"><a class="reference internal" href="release_notes.html">Release notes</a></li>
<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
</ul>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer container">
<a href="http://www.diamond.ac.uk/"><img class="logofooter" alt="Diamond" src="_static/diamond_logo.png" /></a>
<a href="http://dials.diamond.ac.uk/"><img class="logofooter" alt="DIALS" src="_static/dials_logo_fx_transparent_bg.png" /></a>
<a href="http://www.ccp4.ac.uk/"><img class="logofooter" alt="CCP4" src="_static/CCP4-logo-plain.png" /></a>
</div>
<div class="footer">
©2020, Diamond Light Source.
</div>
</body>
</html>