Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-10T12:45:55.980Z
Answers.LastActivityDate: 2023-01-10T12:45:55.980Z
Answers.UserDisplayName: gilleain
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-09T21:27:50.037Z
Comments.Text: Did you read [the paper](https://www.sciencedirect.com/science/article/abs/pii/S0022283698924019) and maybe contact the authors (http://kinemage.biochem.duke.edu/about/) if the paper doesn't make it clear?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-12T12:00:39.567Z
Comments.Text: Are you sure its pdt format and not pdbqt ? (Didnt check , but never found it so far) :https://userguide.mdanalysis.org/1.1.1/formats/reference/pdbqt.html
Comments.UserDisplayName: pippo1980
Tags: <proteins><pdb>
Title: What is changed in this PDB file?
ThreadText: # What is changed in this PDB file?
  
  (Asked by: username_0 on 2023-01-09)
  
  I used [a tool called reduce](https://github.com/rlabduke/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?
  
  **Tags:** proteins, pdb
  
  > **Comments:**
  > **username_1**: Did you read [the paper](https://www.sciencedirect.com/science/article/abs/pii/S0022283698924019) and maybe contact the authors (http://kinemage.biochem.duke.edu/about/) if the paper doesn't make it clear?  
  > **username_2**: Are you sure its pdt format and not pdbqt ? (Didnt check , but never found it so far) :https://userguide.mdanalysis.org/1.1.1/formats/reference/pdbqt.html  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2023-01-10. Score: 6 | Accepted answer
  
  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.
  
  
  ---
  
  