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‎_sources/documentation/programs/dials_import_xds.rst.txt‎

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dials.import_xds
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================
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Introduction
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------------
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.. python_string:: dials.command_line.import_xds.__doc__
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Basic parameters
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----------------
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.. phil:: dials.command_line.import_xds.phil_scope
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:expert-level: 0
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:attributes-level: 0
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Full parameter definitions
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--------------------------
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.. phil:: dials.command_line.import_xds.phil_scope
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:expert-level: 2
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:attributes-level: 2

‎_sources/documentation/programs/index.rst.txt‎

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dials_anvil_correction
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dials_missing_reflections
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dials_filter_reflections
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dials_import_xds
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Printable command line reference:
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‎documentation/conventions.html‎

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<link rel="index" title="Index" href="../genindex.html" />
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‎documentation/programs/dials_filter_reflections.html‎

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<link rel="author" title="About these documents" href="../../about.html" />
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<link rel="index" title="Index" href="../../genindex.html" />
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<link rel="search" title="Search" href="../../search.html" />
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‎documentation/programs/dials_import_xds.html‎

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<!DOCTYPE html>
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<html lang="en" data-content_root="../../">
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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>dials.import_xds &#8212; DIALS documentation</title>
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<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
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<link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
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</head><body>
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<div class="logoheader container">
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<a href="../../index.html">
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<img class="logoheader" alt="DIALS" src="../../_static/dials_header.png" />
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</a>
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</div>
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<div class="document">
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<div class="documentwrapper">
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<div class="bodywrapper">
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<div class="body" role="main">
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<section id="dials-import-xds">
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<h1>dials.import_xds<a class="headerlink" href="#dials-import-xds" title="Link to this heading"></a></h1>
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<section id="introduction">
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<h2>Introduction<a class="headerlink" href="#introduction" title="Link to this heading"></a></h2>
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<p>This program imports xds processed data for use in dials.</p>
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<dl class="simple">
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<dt>It requires up to three things to create an experiment list and reflection table.</dt><dd><ul class="simple">
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<li><p>an XDS.INP, to specify the geometry,</p></li>
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<li><p>one of “INTEGRATE.HKL” or “XPARM.XDS”, which is needed to create the experiment (
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alternatively “XDS_ASCII.HKL” or “GXPARM.XDS” can be specified with xds_file=)</p></li>
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<li><p>INTEGRATE.HKL or SPOT.XDS file to create a reflection table.</p></li>
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</ul>
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</dd>
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</dl>
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<p>To run the program, the easiest thing to do is provide a directory containing these files</p>
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<p>Example use cases:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">dials</span><span class="o">.</span><span class="n">import_xds</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">folder</span><span class="o">/</span><span class="n">containing</span><span class="o">/</span><span class="n">xds</span><span class="o">/</span><span class="n">inp</span><span class="o">/</span> <span class="c1"># Extract all the relevant files from this directory (defaults to importing INTEGRATE.HKL if it exists)</span>
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<span class="n">dials</span><span class="o">.</span><span class="n">import_xds</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">folder</span><span class="o">/</span><span class="n">containing</span><span class="o">/</span><span class="n">xds</span><span class="o">/</span><span class="n">inp</span><span class="o">/</span><span class="n">INTEGRATE</span><span class="o">.</span><span class="n">HKL</span> <span class="c1"># Specify a path to an INTEGRATE.HKL - the XDS.INP must be in the same directory.</span>
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<span class="n">dials</span><span class="o">.</span><span class="n">import_xds</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">folder</span><span class="o">/</span><span class="n">containing</span><span class="o">/</span><span class="n">xds</span><span class="o">/</span><span class="n">inp</span><span class="o">/</span> <span class="n">SPOT</span><span class="o">.</span><span class="n">XDS</span> <span class="c1"># Be explicit about which file to use to create reflections (default is to use INTEGRATE.HKL)</span>
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<span class="n">dials</span><span class="o">.</span><span class="n">import_xds</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">folder</span><span class="o">/</span><span class="n">containing</span><span class="o">/</span><span class="n">xds</span><span class="o">/</span><span class="n">inp</span><span class="o">/</span> <span class="n">xds_file</span><span class="o">=</span><span class="n">XPARM</span><span class="o">.</span><span class="n">XDS</span> <span class="c1"># Specify which extra file should be used to create experiment metadata</span>
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<span class="n">dials</span><span class="o">.</span><span class="n">import_xds</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">folder</span><span class="o">/</span><span class="n">containing</span><span class="o">/</span><span class="n">xds</span><span class="o">/</span><span class="n">inp</span><span class="o">/</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">INTEGRATE</span><span class="o">.</span><span class="n">HKL</span> <span class="c1"># Will take XDS.INP from the directory, and everything else needed from the specified INTEGRATE.HKL file</span>
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</pre></div>
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</div>
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</section>
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<section id="basic-parameters">
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<h2>Basic parameters<a class="headerlink" href="#basic-parameters" title="Link to this heading"></a></h2>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">input</span> <span class="p">{</span>
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<span class="n">xds_file</span> <span class="o">=</span> <span class="kc">None</span>
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<span class="p">}</span>
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<span class="n">output</span> <span class="p">{</span>
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<span class="n">reflections</span> <span class="o">=</span> <span class="kc">None</span>
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<span class="n">xds_experiments</span> <span class="o">=</span> <span class="s2">&quot;xds_models.expt&quot;</span>
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<span class="n">log</span> <span class="o">=</span> <span class="n">dials</span><span class="o">.</span><span class="n">import_xds</span><span class="o">.</span><span class="n">log</span>
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<span class="p">}</span>
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<span class="n">remove_invalid</span> <span class="o">=</span> <span class="kc">False</span>
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<span class="n">add_standard_columns</span> <span class="o">=</span> <span class="kc">False</span>
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<span class="n">read_varying_crystal</span> <span class="o">=</span> <span class="kc">False</span>
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</pre></div>
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</div>
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</section>
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<section id="full-parameter-definitions">
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<h2>Full parameter definitions<a class="headerlink" href="#full-parameter-definitions" title="Link to this heading"></a></h2>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">input</span> <span class="p">{</span>
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<span class="n">xds_file</span> <span class="o">=</span> <span class="kc">None</span>
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<span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Explicitly specify the file to use &quot;</span>
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<span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="n">path</span>
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<span class="p">}</span>
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<span class="n">output</span> <span class="p">{</span>
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<span class="n">reflections</span> <span class="o">=</span> <span class="kc">None</span>
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<span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;The output filname of the reflections file (defaults to either&quot;</span>
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<span class="s2">&quot;integrate_hkl.refl or spot_xds.refl)&quot;</span>
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<span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">str</span>
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<span class="n">xds_experiments</span> <span class="o">=</span> <span class="s2">&quot;xds_models.expt&quot;</span>
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<span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;The output filename of the experiment list created from xds&quot;</span>
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<span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">str</span>
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<span class="n">log</span> <span class="o">=</span> <span class="n">dials</span><span class="o">.</span><span class="n">import_xds</span><span class="o">.</span><span class="n">log</span>
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<span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="n">path</span>
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<span class="p">}</span>
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<span class="n">remove_invalid</span> <span class="o">=</span> <span class="kc">False</span>
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<span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Remove non-index reflections (if miller indices are present)&quot;</span>
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<span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">bool</span>
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<span class="n">add_standard_columns</span> <span class="o">=</span> <span class="kc">False</span>
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<span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Add empty standard columns to the reflections. Note columns for&quot;</span>
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<span class="s2">&quot;centroid variances are set to contain 1s, not 0s&quot;</span>
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<span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">bool</span>
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<span class="n">read_varying_crystal</span> <span class="o">=</span> <span class="kc">False</span>
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<span class="o">.</span><span class="n">help</span> <span class="o">=</span> <span class="s2">&quot;Attempt to create a scan-varying crystal model from INTEGRATE.LP,&quot;</span>
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<span class="s2">&quot;if present&quot;</span>
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<span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="nb">bool</span>
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</pre></div>
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</div>
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‎documentation/programs/index.html‎

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<li class="toctree-l1"><a class="reference internal" href="dials_anvil_correction.html">dials.anvil_correction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dials_missing_reflections.html">dials.missing_reflections</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dials_filter_reflections.html">dials.filter_reflections</a></li>
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<p>Printable command line reference:</p>

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