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quick_start.html
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<!DOCTYPE html>
<html lang="en" data-content_root="./">
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<meta charset="utf-8" />
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<title>Quick start guide — xia2 documentation</title>
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<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>
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<h3>Navigation</h3>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Getting started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="insulin_tutorial.html">Insulin tutorial</a></li>
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<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>
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