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  <section id="parameters">
<h1>Parameters<a class="headerlink" href="#parameters" title="Link to this heading">¶</a></h1>
<section id="commonly-used-program-options">
<h2>Commonly used program options<a class="headerlink" href="#commonly-used-program-options" title="Link to this heading">¶</a></h2>
<p>There are a number of program options used on a daily basis in xia2, which
are:</p>
<blockquote>
<div><table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">atom=X</span></code></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-even"><td><p><code class="docutils literal notranslate"><span class="pre">pipeline=3d</span></code></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-odd"><td><p><code class="docutils literal notranslate"><span class="pre">pipeline=3dii</span></code></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>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">pipeline=dials</span></code></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-odd"><td><p><code class="docutils literal notranslate"><span class="pre">pipeline=dials-aimless</span></code></p></td>
<td><p>Tell xia2 to use <a class="reference external" href="http://dials.github.io/">DIALS</a> but scale with <a class="reference external" href="http://www.ccp4.ac.uk/html/aimless.html">Aimless</a>.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">xinfo=some.xinfo</span></code></p></td>
<td><p>Use specific modified .xinfo input file.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">image=/path/to/an/image.img</span></code></p></td>
<td><p>Process a specific scan.  Pass multiple <code class="docutils literal notranslate"><span class="pre">image=</span></code> parameters to include multiple scans.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">image=/path/to/an/image.img:start:end</span></code></p></td>
<td><p>Process a specific image range within a scan.  <code class="docutils literal notranslate"><span class="pre">start</span></code> and <code class="docutils literal notranslate"><span class="pre">end</span></code> are numbers denoting the image range, e.g. <code class="docutils literal notranslate"><span class="pre">image=/path/to/an/image.img:1:100</span></code> processes images 1–100 inclusive.  As above, one can pass multiple <code class="docutils literal notranslate"><span class="pre">image=</span></code> parameters.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">small_molecule=true</span></code></p></td>
<td><p>Process in manner more suited to small molecule data.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">space_group=sg</span></code></p></td>
<td><p>Set the spacegroup, e.g. <code class="docutils literal notranslate"><span class="pre">P21</span></code>.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">unit_cell=a,b,c,α,β,γ</span></code></p></td>
<td><p>Set the cell constants.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">hdf5_plugin=/path/to/durin.so</span></code></p></td>
<td><p>Set the path to the HDF5 file reading plugin for XDS (needed for processing of Eiger data)</p></td>
</tr>
</tbody>
</table>
</div></blockquote>
</section>
<section id="resolution-limits">
<h2>Resolution limits<a class="headerlink" href="#resolution-limits" title="Link to this heading">¶</a></h2>
<p>xia2 uses <code class="docutils literal notranslate"><span class="pre">dials.estimate_resolution</span></code> to estimate the resolution limit, sharing the
same parameters and defaults.
The default behaviour (<code class="docutils literal notranslate"><span class="pre">cc_half=0.3</span></code>) can be overridden with e.g.:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>xia2<span class="w"> </span><span class="o">[</span>options<span class="o">]</span><span class="w"> </span><span class="nv">cc_half</span><span class="o">=</span>None<span class="w"> </span><span class="nv">misigma</span><span class="o">=</span><span class="m">1</span><span class="w"> </span><span class="nv">isigma</span><span class="o">=</span><span class="m">0</span>.25
</pre></div>
</div>
<p>See the <a class="reference external" href="https://dials.github.io/documentation/programs/dials_estimate_resolution.html">dials.estimate_resolution</a> documentation for further details.</p>
</section>
<section id="phil-parameters">
<h2>Phil parameters<a class="headerlink" href="#phil-parameters" title="Link to this heading">¶</a></h2>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>We have now moved towards moving <a class="reference external" href="http://cctbx.sourceforge.net/libtbx_phil.html">PHIL (Python-based Hierarchial Interchange Language)</a>
for specifying xia2 program parameters,
which will in the long run help the documentation, but in the mean time you may see some
warnings as certain parameters were changed from <code class="samp docutils literal notranslate"><span class="pre">-param</span></code> style parameters to
<code class="samp docutils literal notranslate"><span class="pre">param=</span></code> style PHIL parameters. If you see, e.g.:</p>
<blockquote>
<div><p><code class="samp docutils literal notranslate"><span class="pre">Warning:</span> <span class="pre">-spacegroup</span> <span class="pre">option</span> <span class="pre">deprecated:</span> <span class="pre">please</span> <span class="pre">use</span> <span class="pre">space_group='P422'</span> <span class="pre">instead</span></code></p>
<p><code class="samp docutils literal notranslate"><span class="pre">Warning:</span> <span class="pre">-resolution</span> <span class="pre">option</span> <span class="pre">deprecated:</span> <span class="pre">please</span> <span class="pre">use</span> <span class="pre">d_min=1.5</span> <span class="pre">instead</span></code></p>
<p><code class="samp docutils literal notranslate"><span class="pre">Command</span> <span class="pre">line</span> <span class="pre">option</span> <span class="pre">-3d</span> <span class="pre">is</span> <span class="pre">deprecated.</span> <span class="pre">Please</span> <span class="pre">use</span> <span class="pre">pipeline=3d</span> <span class="pre">instead</span></code></p>
</div></blockquote>
<p>don’t panic - this is to be expected - but you may want to change the way you run xia2
or your scripts. More of a warning for beamline / automation people! The outcome of this
should however be automated generation of command-line documentation and the ability to
keep “recipes” for running xia2 in tidy files.</p>
</div>
<p>Here is a comprehensive list of PHIL parameters used by xia2:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">general</span> <span class="p">{</span>
<span class="p">}</span>
<span class="n">xds</span> <span class="p">{</span>
  <span class="n">keep_outliers</span> <span class="o">=</span> <span class="kc">True</span>
  <span class="n">correct</span> <span class="p">{</span>
  <span class="p">}</span>
  <span class="n">integrate</span> <span class="p">{</span>
  <span class="p">}</span>
  <span class="n">init</span> <span class="p">{</span>
  <span class="p">}</span>
  <span class="n">defpix</span> <span class="p">{</span>
  <span class="p">}</span>
  <span class="n">index</span> <span class="p">{</span>
    <span class="n">max_wedge_size</span> <span class="o">=</span> <span class="mi">5</span>
    <span class="n">max_wedge_size_degrees</span> <span class="o">=</span> <span class="kc">None</span>
  <span class="p">}</span>
  <span class="n">colspot</span> <span class="p">{</span>
  <span class="p">}</span>
  <span class="n">xscale</span> <span class="p">{</span>
  <span class="p">}</span>
  <span class="n">merge2cbf</span> <span class="p">{</span>
  <span class="p">}</span>
<span class="p">}</span>
<span class="n">dials</span> <span class="p">{</span>
  <span class="n">outlier</span> <span class="p">{</span>
  <span class="p">}</span>
  <span class="n">find_spots</span> <span class="p">{</span>
    <span class="n">filter_ice_rings</span> <span class="o">=</span> <span class="kc">False</span>
  <span class="p">}</span>
  <span class="n">index</span> <span class="p">{</span>
    <span class="n">method</span> <span class="o">=</span> <span class="n">fft1d</span> <span class="o">*</span><span class="n">fft3d</span> <span class="n">real_space_grid_search</span>
    <span class="n">max_cell_estimation</span> <span class="p">{</span>
    <span class="p">}</span>
  <span class="p">}</span>
<span class="p">}</span>
<span class="n">xia2</span><span class="o">.</span><span class="n">settings</span> <span class="p">{</span>
  <span class="n">pipeline</span> <span class="o">=</span> <span class="mi">3</span><span class="n">d</span> <span class="mi">3</span><span class="n">dd</span> <span class="mi">3</span><span class="n">di</span> <span class="mi">3</span><span class="n">dii</span> <span class="o">*</span><span class="n">dials</span> <span class="n">dials</span><span class="o">-</span><span class="n">aimless</span>
  <span class="n">project</span> <span class="o">=</span> <span class="s1">'AUTOMATIC'</span>
  <span class="n">crystal</span> <span class="o">=</span> <span class="s1">'DEFAULT'</span>
  <span class="nb">input</span> <span class="p">{</span>
    <span class="n">atom</span> <span class="o">=</span> <span class="kc">None</span>
    <span class="n">anomalous</span> <span class="o">=</span> <span class="n">Auto</span>
  <span class="p">}</span>
  <span class="n">space_group</span> <span class="o">=</span> <span class="kc">None</span>
  <span class="n">unit_cell</span> <span class="o">=</span> <span class="kc">None</span>
  <span class="n">resolution</span> <span class="p">{</span>
    <span class="n">keep_all_reflections</span> <span class="o">=</span> <span class="n">Auto</span>
    <span class="n">d_max</span> <span class="o">=</span> <span class="kc">None</span>
    <span class="n">d_min</span> <span class="o">=</span> <span class="kc">None</span>
    <span class="n">cc_half_method</span> <span class="o">=</span> <span class="o">*</span><span class="n">half_dataset</span> <span class="n">sigma_tau</span>
    <span class="n">reflections_per_bin</span> <span class="o">=</span> <span class="mi">10</span>
    <span class="n">labels</span> <span class="o">=</span> <span class="kc">None</span>
    <span class="n">reference</span> <span class="o">=</span> <span class="kc">None</span>
    <span class="n">emax</span> <span class="o">=</span> <span class="mi">4</span>
  <span class="p">}</span>
  <span class="n">multiprocessing</span> <span class="p">{</span>
    <span class="n">nproc</span> <span class="o">=</span> <span class="n">Auto</span>
  <span class="p">}</span>
  <span class="n">symmetry</span> <span class="p">{</span>
    <span class="n">chirality</span> <span class="o">=</span> <span class="n">chiral</span> <span class="n">nonchiral</span> <span class="n">centrosymmetric</span>
    <span class="n">program</span> <span class="o">=</span> <span class="o">*</span><span class="n">pointless</span> <span class="n">dials</span>
  <span class="p">}</span>
  <span class="n">output</span> <span class="p">{</span>
    <span class="n">mmcif</span> <span class="p">{</span>
    <span class="p">}</span>
  <span class="p">}</span>
<span class="p">}</span>
</pre></div>
</div>
</section>
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