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rebuilt html docs for version 2.11.0-dev0 from branch develop with sphinx at 12dcfc3 
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‎2.11.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf‎

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‎2.11.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html‎

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‎2.11.0-dev0/examples/constructing_universe.html‎

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@@ -715,7 +715,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
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<li><p>NMP: residues 30-59 (blue)</p></li>
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<li><p>LID: residues 122-159 (yellow)</p></li>
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</ul>
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<p><img alt="4b530786ccbb4e80b5173ac9005cae3b" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
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<p><img alt="4d365d6c9c8242cb801f8a054e870d9b" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
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<div class="nbinput docutils container">
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<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[26]:
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</pre></div>

‎2.11.0-dev0/formats/auxiliary.html‎

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@@ -261,7 +261,7 @@ <h2>Reading data directly<a class="headerlink" href="#reading-data-directly" tit
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<span class="gp">In [3]: </span><span class="n">aux</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="n">XVG_BZ2</span><span class="p">)</span>
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<span class="gp">In [4]: </span><span class="n">aux</span>
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<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9c7870d190&gt;</span>
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<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fefa9dc1d60&gt;</span>
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</pre></div>
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</div>
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<p>In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.</p>
@@ -460,7 +460,7 @@ <h2>Recreating auxiliaries<a class="headerlink" href="#recreating-auxiliaries" t
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<span class="gp">In [30]: </span><span class="k">del</span> <span class="n">aux</span>
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<span class="gp">In [31]: </span><span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="o">**</span><span class="n">description</span><span class="p">)</span>
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<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9c78cdf620&gt;</span>
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<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fefa9f64140&gt;</span>
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</pre></div>
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</div>
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<p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
@@ -575,7 +575,7 @@ <h2>Standalone Usage<a class="headerlink" href="#standalone-usage" title="Link t
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<div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [45]: </span><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
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<span class="gp">In [46]: </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Time&quot;</span><span class="p">],</span> <span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Temperature&quot;</span><span class="p">])</span>
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<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f9c727261b0&gt;]</span>
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<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fefa8eb0aa0&gt;]</span>
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<span class="gp">In [47]: </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Temperature [K]&quot;</span><span class="p">)</span>
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<span class="gh">Out[47]: </span><span class="go">Text(0, 0.5, &#39;Temperature [K]&#39;)</span>

‎2.11.0-dev0/guessing.html‎

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@@ -379,7 +379,7 @@ <h3>Order of guessing<a class="headerlink" href="#order-of-guessing" title="Link
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<span class="g g-Whitespace"> </span><span class="mi">449</span> <span class="n">lower_bound</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;lower_bound&quot;</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
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<span class="g g-Whitespace"> </span><span class="mi">451</span> <span class="n">box</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;box&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
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<span class="ne">ValueError</span>: vdw radii for types: 72, 6, 54, 7, 26, 24, 25, 10, 5, 56, 2, 21, 57, 29, 32, 52, 50, 55, 31, 81, 30, 3, 51, 1, 20, 9, 22, 70, 73, 23. These can be defined manually using the keyword &#39;vdwradii&#39;
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<span class="ne">ValueError</span>: vdw radii for types: 29, 7, 22, 3, 24, 73, 32, 57, 30, 26, 54, 72, 6, 31, 70, 1, 56, 23, 10, 5, 9, 81, 51, 55, 50, 21, 20, 52, 2, 25. These can be defined manually using the keyword &#39;vdwradii&#39;
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</pre></div>
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</div>
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<p>However, the snippet below will re-guess the types, and now bond-guessing can work as the elements have vdW radii defined:</p>

‎2.11.0-dev0/index.html‎

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<section id="welcome-to-mdanalysis-user-guide-s-documentation">
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<h1>Welcome to MDAnalysis User Guide’s documentation!<a class="headerlink" href="#welcome-to-mdanalysis-user-guide-s-documentation" title="Link to this heading"></a></h1>
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<p><strong>MDAnalysis version:</strong> 2.11.0-dev0</p>
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<p><strong>Last updated:</strong> Nov 18, 2025</p>
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<p><strong>Last updated:</strong> Nov 21, 2025</p>
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<p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is a Python
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toolkit to analyse molecular dynamics files and trajectories in <a class="reference internal" href="formats/index.html#formats"><span class="std std-ref">many popular formats</span></a>. MDAnalysis can write
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most of these formats, too, together with atom selections for use in <a class="reference internal" href="formats/selection_exporters.html#selection-exporters"><span class="std std-ref">visualisation tools or other analysis programs</span></a>.

‎2.11.0-dev0/reading_and_writing.html‎

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<span class="gp">In [16]: </span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
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<span class="gh">Out[16]: </span>
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<span class="go">array([[0.26797223, 0.38690624, 0.69587946],</span>
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<span class="go"> [0.16045298, 0.42770648, 0.23505129],</span>
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<span class="go"> [0.704188 , 0.7275821 , 0.91988504],</span>
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<span class="go">array([[0.74751663, 0.24898715, 0.94400805],</span>
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<span class="go"> [0.9995619 , 0.22681649, 0.47731233],</span>
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<span class="go"> [0.04954287, 0.41348678, 0.13441835],</span>
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<span class="go"> ...,</span>
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<span class="go"> [0.9841226 , 0.33841234, 0.36142474],</span>
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<span class="go"> [0.74384415, 0.7097269 , 0.19336794],</span>
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<span class="go"> [0.34026566, 0.78603977, 0.53190196]],</span>
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<span class="go"> [0.92856705, 0.25478333, 0.93481356],</span>
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<span class="go"> [0.5756663 , 0.22680707, 0.9727279 ],</span>
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<span class="go"> [0.96631837, 0.7568849 , 0.28422678]],</span>
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<span class="go"> shape=(47681, 3), dtype=float32)</span>
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</pre></div>
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</div>
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<span class="gp">In [18]: </span><span class="n">universe2</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
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<span class="gh">Out[18]: </span>
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<span class="go">array([[0.26797223, 0.38690624, 0.69587946],</span>
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<span class="go"> [0.16045298, 0.42770648, 0.23505129],</span>
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<span class="go"> [0.704188 , 0.7275821 , 0.91988504],</span>
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<span class="go">array([[0.74751663, 0.24898715, 0.94400805],</span>
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<span class="go"> [0.9995619 , 0.22681649, 0.47731233],</span>
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<span class="go"> [0.04954287, 0.41348678, 0.13441835],</span>
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<span class="go"> ...,</span>
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<span class="go"> [0.9841226 , 0.33841234, 0.36142474],</span>
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<span class="go"> [0.74384415, 0.7097269 , 0.19336794],</span>
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<span class="go"> [0.34026566, 0.78603977, 0.53190196]],</span>
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<span class="go"> [0.92856705, 0.25478333, 0.93481356],</span>
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<span class="go"> [0.5756663 , 0.22680707, 0.9727279 ],</span>
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<span class="go"> [0.96631837, 0.7568849 , 0.28422678]],</span>
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<span class="go"> shape=(47681, 3), dtype=float32)</span>
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</pre></div>
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</div>

‎2.11.0-dev0/searchindex.js‎

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‎2.11.0-dev0/standard_selections.html‎

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@@ -332,10 +332,10 @@ <h3>Protein backbone<a class="headerlink" href="#protein-backbone" title="Link t
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<p>Protein backbone atoms in MDAnalysis belong to a recognised protein residue and have the atom names:</p>
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<table class="docutils align-default">
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<tbody>
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<tr class="row-odd"><td><p>N</p></td>
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<td><p>C</p></td>
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<td><p>CA</p></td>
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<tr class="row-odd"><td><p>CA</p></td>
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<td><p>C</p></td>
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</tbody>
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<p>The below names are drawn from largely from the CHARMM force field.</p>
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<table class="docutils align-default">
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<tbody>
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<tr class="row-odd"><td><p>CYT</p></td>
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<td><p>RA</p></td>
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<td><p>DG3</p></td>
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<td><p>RU3</p></td>
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<td><p>T</p></td>
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<tr class="row-odd"><td><p>RU5</p></td>
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<td><p>RC</p></td>
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<td><p>U</p></td>
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<td><p>DA3</p></td>
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</tr>
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<tr class="row-even"><td><p>DC</p></td>
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<td><p>DG</p></td>
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<td><p>RG</p></td>
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<td><p>DC3</p></td>
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<td><p>RC5</p></td>
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<td><p>GUA</p></td>
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<td><p>RA3</p></td>
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<td><p>RA</p></td>
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<td><p>RC3</p></td>
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<td><p>RU</p></td>
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<td><p>RU</p></td>
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<td><p>GUA</p></td>
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<td><p>RC5</p></td>
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</tr>
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<tr class="row-even"><td><p>T</p></td>
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<td><p>DG</p></td>
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<td><p>ADE</p></td>
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<td><p>URA</p></td>
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<td><p>DT3</p></td>
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<td><p>RG3</p></td>
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<td><p>DA5</p></td>
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<td><p>A</p></td>
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<td><p>DT5</p></td>
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<td><p>DA</p></td>
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<td><p>RG5</p></td>
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</tr>
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<tr class="row-odd"><td><p>RU3</p></td>
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<td><p>DA3</p></td>
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<td><p>DC3</p></td>
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<td><p>C</p></td>
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<td><p>RA5</p></td>
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<td><p>RG5</p></td>
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<td><p>DC</p></td>
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<td><p>DA</p></td>
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<td><p>RA3</p></td>
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</tr>
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<tr class="row-even"><td><p>DT</p></td>
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<td><p>CYT</p></td>
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<td><p>U</p></td>
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<td><p>G</p></td>
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<td><p>ADE</p></td>
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<td><p>RG3</p></td>
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<td><p>THY</p></td>
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<td><p>RG</p></td>
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<td><p>DC5</p></td>
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<td><p>RA5</p></td>
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</tr>
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<tr class="row-odd"><td><p>A</p></td>
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<td><p>DA5</p></td>
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<tr class="row-odd"><td><p>DG3</p></td>
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<td><p>DT3</p></td>
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<td></td>
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<td></td>
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<td></td>
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<p>Nucleic backbone atoms in MDAnalysis belong to a recognised nucleic acid residue and have the atom names:</p>
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<table class="docutils align-default">
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<tbody>
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<tr class="row-odd"><td><p>C3’</p></td>
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<tr class="row-odd"><td><p>P</p></td>
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<td><p>C5’</p></td>
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<td><p>O3’</p></td>
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<td><p>P</p></td>
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<td><p>O5’</p></td>
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<td><p>C5’</p></td>
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<td><p>C3’</p></td>
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</tr>
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</tbody>
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<p>Nucleobase atoms from nucleic acid residues are recognised based on their names in CHARMM.</p>
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<table class="docutils align-default">
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<tr class="row-odd"><td><p>N2</p></td>
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<td><p>N3</p></td>
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<tr class="row-odd"><td><p>C4</p></td>
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<td><p>C5</p></td>
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<td><p>C2</p></td>
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<td><p>O6</p></td>
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<td><p>N4</p></td>
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<td><p>C5M</p></td>
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<td><p>N9</p></td>
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</tr>
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<tr class="row-even"><td><p>O2</p></td>
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<td><p>C6</p></td>
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<td><p>C5M</p></td>
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<td><p>C8</p></td>
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<td><p>N6</p></td>
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<td><p>O6</p></td>
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</tr>
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<tr class="row-even"><td><p>N2</p></td>
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<td><p>N3</p></td>
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<td><p>N7</p></td>
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<td><p>N4</p></td>
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<td><p>N1</p></td>
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<td><p>C4</p></td>
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<td><p>O4</p></td>
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<td><p>C8</p></td>
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<td><p>N7</p></td>
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<td><p>N9</p></td>
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<td><p>O2</p></td>
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</tbody>
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</table>
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<p>Nucleic sugar atoms from nucleic acid residues are recognised by MDAnalysis if they have the atom names:</p>
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<table class="docutils align-default">
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<tbody>
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<tr class="row-odd"><td><p>C3’</p></td>
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<td><p>C4’</p></td>
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<td><p>O4’</p></td>
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<tr class="row-odd"><td><p>O4’</p></td>
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<td><p>C2’</p></td>
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<td><p>C4’</p></td>
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<td><p>C3’</p></td>
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<td><p>C1’</p></td>
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