atlas/table_user.html at master · agchempa/atlas · GitHub

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<!DOCTYPE html>
<html lang="en">
<head>
  <title>Contact comparison atlas - G-proteins</title>
  <meta charset="UTF-8">
  <meta name="viewport" content="width=device-width, initial-scale=1">

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<body>

<header>
  <div class="jumbotron">
    <div class="container">
      <h1 class="display-3">Contact comparison atlas</h1>
      <p>Table of user-defined structures</p>
    </div>
  </div>
</header>

<div class="container" id="userTableContents"></div>
<div class="container" id="tableContents"></div>

<script>
  createUserUpload("#userTableContents");
</script>

<section>
  <div class="container">
    <div class="row">
      <h4>How to compare your structures and identify interaction patterns?</h4>
      <p>
        You can do this in three simple steps:
      </p>
      <ol>
        <li>Generate structural alignment and map structurally equivalent positions</li>
        <li>Compute interactions</li>
        <li>Interactively visualize interaction patterns</li>
      </ol>
      <p>
        The following example compares the two structures with PDB ids 2RH1 and 3UON:
      </p>
      <ol>
        <li>Generate structural alignment and map structurally equivalent positions</li>
        <ul>
          <li>Prepare your structures by adding hydrogen. This can be done using e.g. pymol.</li>
          <li>Save the structures that have hydrogens added to them: 3UON_h_added.pdb
            and 2RH1_h_added.pdb.</li>
          <li>Generate a multiple sequence alignment using Gesamt (v1.09/v1.15) from
            CCP4 (<a href="http://www.ccp4.ac.uk/">www.ccp4.ac.uk</a>) and save the output:<br>
            <code>$ gesamt 3UON_h_added.pdb 2RH1_h_added.pdb &gt; output.txt</code>
          </li>
          <li>Generate residue-label files using <code>get_resilabels.py</code><br>
            <code>$ get_resilabels.py --input_gesamt output.txt --output_path label_files/
              --proteins 3UON 2RH1</code>
          </li>
        </ul>
        <li>Compute interactions using Getcontacts:</li>
        <ul>
          <li><code>$ get_static_contacts.py --structure 3UON_h_added.pdb --output
            3UON_contacts.tsv --itypes all</code></li>
          <li><code>$ get_static_contacts.py --structure 2RH1_h_added.pdb --output
            2RH1_contacts.tsv --itypes all</code></li>
        </ul>
        <li>Using this webpage, upload the the pdb files and the above-generated interaction
          files and label files.</li>
      </ol>
      </p>
    </div>
  </div>
</section>

</body>
</html>