Answers.Body: <p>The <code>sequence_n.pdb</code> files are temporary and are combined into an <code>ensemble.i.pdb</code> file after each iteration <code>i</code>. That file has many structures in. After the run is complete there will be a <code>final_1.pdb</code> file. Don't worry about the cluster files. If you are interested in what they do, consult the <code>run_dmpfold.sh</code> script and see what it is doing line by line.</p>
  
  <p>As I have said multiple times elsewhere, you should run the script with default parameters and let it run <em>to completion</em>. Then use the <code>final_1.pdb</code> and any other <code>final_*.pdb</code> files as the output. If you want more structures, use the <code>ensemble.i.pdb</code> files.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-17T11:13:42.957Z
Answers.LastActivityDate: 2019-09-17T11:13:42.957Z
Answers.UserDisplayName: jgreener
Body: <p>I ran this command:</p>
  
  <pre><code>run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./folder 10 500 
  </code></pre>
  
  <p>From my previous discussion, I understand that I should run with default "run_dmpfold.sh" parameters i.e. <code>3 50</code>; however, since I have already run the <code>10 500</code> I have some questions.</p>
  
  <p>I see that after generating "sequence_1.pdb to sequence_500.pdb" files, these files are no more in the folder and, now I see "ensemble_1.pdb". 
  Will there be more ensemble files like "ensemble_500.pdb" and "sequence_n.pdb" files? I mean when can I expect "final_1.pdb' file? Also, I see files like "CLUSTERS_001.pdb".</p>
  
Tags: <protein-structure>
Title: DMPfold: number of models produced using "10 500" feature in "run_dmpfold.sh"?
ThreadText: # DMPfold: number of models produced using "10 500" feature in "run_dmpfold.sh"?
  
  (Asked by: username_0 on 2019-09-17)
  
  I ran this command:
  
  ```
  run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./folder 10 500 
  
  ```
  
  From my previous discussion, I understand that I should run with default "run\_dmpfold.sh" parameters i.e. `3 50`; however, since I have already run the `10 500` I have some questions.
  
  I see that after generating "sequence\_1.pdb to sequence\_500.pdb" files, these files are no more in the folder and, now I see "ensemble\_1.pdb".
  Will there be more ensemble files like "ensemble\_500.pdb" and "sequence\_n.pdb" files? I mean when can I expect "final\_1.pdb' file? Also, I see files like "CLUSTERS\_001.pdb".
  
  **Tags:** protein-structure
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-09-17. Score: 0 | Accepted answer
  
  The `sequence_n.pdb` files are temporary and are combined into an `ensemble.i.pdb` file after each iteration `i`. That file has many structures in. After the run is complete there will be a `final_1.pdb` file. Don't worry about the cluster files. If you are interested in what they do, consult the `run_dmpfold.sh` script and see what it is doing line by line.
  
  As I have said multiple times elsewhere, you should run the script with default parameters and let it run *to completion*. Then use the `final_1.pdb` and any other `final_*.pdb` files as the output. If you want more structures, use the `ensemble.i.pdb` files.
  
  
  ---
  
  