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<!DOCTYPE html>
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<title>Using xia2 — xia2 documentation</title>
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<section id="using-xia2">
<h1>Using xia2<a class="headerlink" href="#using-xia2" title="Link to this heading">¶</a></h1>
<p>As mentioned in the <a class="reference internal" href="quick_start.html"><span class="doc">quick start guide</span></a>, to get started simply run:</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>The program is used from the command-line; there is no GUI. The
most important command-line options are as follows:</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> with DIALS scaling</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>These specify in the broadest possible terms to the program the manner
in which you would like the processing performed. The program will then
read all of the image headers found in <code class="samp docutils literal notranslate"><span class="pre">/here/are/my/data</span></code> to organise the
data, first into sweeps, then into wavelengths, before assigning all of these
wavelengths to a crystal.</p>
<p>The data from the experiment is understood as follows. The SWEEP,
which corresponds to one “scan”, is the basic unit of indexing and integration.
These are contained by WAVELENGTH objects which correspond to
CCP4 MTZ datasets, and will ultimately have unique Miller indices. For
example, a low and high dose pass will be merged together. A CRYSTAL
however contains all of the data from the experiment and is the basic unit of
data for scaling. This description of the experiment is written automatically
to an instruction file, an example of which is shown in below:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">BEGIN</span> <span class="n">PROJECT</span> <span class="n">AUTOMATIC</span>
<span class="n">BEGIN</span> <span class="n">CRYSTAL</span> <span class="n">DEFAULT</span>
<span class="n">BEGIN</span> <span class="n">HA_INFO</span>
<span class="n">ATOM</span> <span class="n">Ba</span>
<span class="n">END</span> <span class="n">HA_INFO</span>
<span class="n">BEGIN</span> <span class="n">WAVELENGTH</span> <span class="n">SAD</span>
<span class="n">WAVELENGTH</span> <span class="mf">0.979500</span>
<span class="n">END</span> <span class="n">WAVELENGTH</span> <span class="n">SAD</span>
<span class="n">BEGIN</span> <span class="n">SWEEP</span> <span class="n">SWEEP1</span>
<span class="n">WAVELENGTH</span> <span class="n">SAD</span>
<span class="n">DIRECTORY</span> <span class="o">/</span><span class="n">dls</span><span class="o">/</span><span class="n">i02</span><span class="o">/</span><span class="n">data</span><span class="o">/</span><span class="mi">2011</span><span class="o">/</span><span class="n">mx1234</span><span class="o">-</span><span class="mi">5</span>
<span class="n">IMAGE</span> <span class="n">K5_M1S3_3_001</span><span class="o">.</span><span class="n">img</span>
<span class="n">START_END</span> <span class="mi">1</span> <span class="mi">450</span>
<span class="n">END</span> <span class="n">SWEEP</span> <span class="n">SWEEP1</span>
<span class="n">END</span> <span class="n">CRYSTAL</span> <span class="n">DEFAULT</span>
<span class="n">END</span> <span class="n">PROJECT</span> <span class="n">AUTOMATIC</span>
</pre></div>
</div>
<p>The input file to the program, which is generated automatically,
shows how the input data are understood. This may be adjusted and the
program rerun, which will be covered in more detail later in the manual.</p>
</section>
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<h3>Navigation</h3>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="quick_start.html">Getting started</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">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="serial_crystallography.html">Serial-crystallography</a></li>
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<li class="toctree-l1"><a class="reference internal" href="parameters.html">Parameters</a></li>
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<li class="toctree-l1"><a class="reference internal" href="acknowledgements.html">Acknowledgements</a></li>
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