text: user5180: I ran dmpfold using this command:
  run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log
  
  It produced files like this:
  sequence_sub_embed_1.pdb ..... sequence_sub_embed_500.pdb
  And, now I see some more files like this being produced:
  sequence_1.pdb .... sequence_2.pdb .....etc
  Can you please let me know what is dmpfold doing here? And can I stop dmpfold in between when desired number of models are generated? And, while it is running, can I move the previously made pdbs to new location becuase of disk space issues or all pdbs have to be in the "dmpfold-lysin" as stated in the command-line above? Thanks.
  
  user4622: From the docs:
  
  The final model is final_1.pdb and other structures may or may not be generated as final_2.pdb to final_5.pdb if they are significantly different. Many other files are generated totalling around 100 MB - these should be deleted to save disk space if you are running DMPfold on many sequences.
  
  These other files include intermediate CNS files (sequence_sub_embed_1.pdb etc.), output files before clustering (sequence_1.pdb etc.) and saved ensembles of previous iterations (ensemble.1.pdb etc.).
  Let the run finish or you won't get the final output files. If you want to use all the generated structures, use the ensemble.n.pdb file from the last iteration (i.e. the highest number). You can also use the other ensemble files if you want to include models from previous iterations.
  I would strongly recommend using default "3 50" parameters until you get things working. Don't move files during the run. You really don't get much benefit of going beyond 50 models per iteration, trust me. We tried it relatively extensively!
  
original_text: 5180: <p>I ran dmpfold using this command:</p>
  
  <pre><code>run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &amp;&gt; dmpfold-log.log
  </code></pre>
  
  <p>It produced files like this:</p>
  
  <p>sequence_sub_embed_1.pdb ..... sequence_sub_embed_500.pdb</p>
  
  <p>And, now I see some more files like this being produced:</p>
  
  <p>sequence_1.pdb .... sequence_2.pdb .....etc</p>
  
  <p>Can you please let me know what is dmpfold doing here? And can I stop dmpfold in between when desired number of models are generated? And, while it is running, can I move the previously made pdbs to new location becuase of disk space issues or all pdbs have to be in the "dmpfold-lysin" as stated in the command-line above? Thanks.</p>
   4622: <p>From the <a href="https://github.com/psipred/DMPfold" rel="nofollow noreferrer">docs</a>:</p>
  
  <blockquote>
    <p>The final model is <code>final_1.pdb</code> and other structures may or may not be generated as <code>final_2.pdb</code> to <code>final_5.pdb</code> if they are significantly different. Many other files are generated totalling around 100 MB - these should be deleted to save disk space if you are running DMPfold on many sequences.</p>
  </blockquote>
  
  <p>These other files include intermediate CNS files (<code>sequence_sub_embed_1.pdb</code> etc.), output files before clustering (<code>sequence_1.pdb</code> etc.) and saved ensembles of previous iterations (<code>ensemble.1.pdb</code> etc.).</p>
  
  <p>Let the run finish or you won't get the final output files. If you want to use all the generated structures, use the <code>ensemble.n.pdb</code> file from the last iteration (i.e. the highest number). You can also use the other ensemble files if you want to include models from previous iterations.</p>
  
  <p>I would strongly recommend using default "3 50" parameters until you get things working. Don't move files during the run. You really don't get much benefit of going beyond 50 models per iteration, trust me. We tried it relatively extensively!</p>
  