text: user12686: I used a tool called reduce to add Hydrogen bonds information to the PDB file.
  I used the command:
  $ ./reduce -NOFLIP 2GB1.pdb > 2GB1_with_H.pdb
  
  The output file is supplied as follows:
  
  https://textdoc.co/ZiuA0tY2elnoh5VK
  
  I haven't understood the output.
  What special change was made by the tool to the 2GB1.pdb file?
  
  user745: So the 'right' answer here would be for you to use a diff tool of some kind (WinDiff, or just the diff command in a Unix-like environment). That would show you the exact added lines. (Although, trying this myself does not produce very clear results...)
  However, I know from running reduce on PDB files that it's added a few things:
  
  The "USER MOD" lines, there's one on the first line and a large block just before the ATOM records
  The hydrogen atoms, of course, needed for correct H-bond calculations
  
  As some commenters have pointed out, this should really be in the paper or other documentation for the tool.
  
original_text: 12686: <p>I used <a href="https://github.com/rlabduke/reduce" rel="nofollow noreferrer">a tool called reduce</a> to add Hydrogen bonds information to the PDB file.</p>
  <p>I used the command:</p>
  <pre><code>$ ./reduce -NOFLIP 2GB1.pdb &gt; 2GB1_with_H.pdb
  </code></pre>
  <p>The output file is supplied as follows:</p>
  <ul>
  <li><a href="https://textdoc.co/ZiuA0tY2elnoh5VK" rel="nofollow noreferrer">https://textdoc.co/ZiuA0tY2elnoh5VK</a></li>
  </ul>
  <p>I haven't understood the output.</p>
  <p>What special change was made by the tool to the <code>2GB1.pdb</code> file?</p>
   745: <p>So the 'right' answer here would be for you to use a <code>diff</code> tool of some kind (WinDiff, or just the diff command in a Unix-like environment). That would show you the exact added lines. (Although, trying this myself does not produce very clear results...)</p>
  <p>However, I know from running <code>reduce</code> on PDB files that it's added a few things:</p>
  <ul>
  <li>The &quot;USER MOD&quot; lines, there's one on the first line and a large block just before the ATOM records</li>
  <li>The hydrogen atoms, of course, needed for correct H-bond calculations</li>
  </ul>
  <p>As some commenters have pointed out, this should really be in the paper or other documentation for the tool.</p>
  