Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-12T17:10:11.163Z
Answers.Text: Just one question: "output files before clustering" and "ensemble files": are these also 500 + 500 in number?
Answers.UserDisplayName: DanielSebas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-12T17:18:52.480Z
Answers.Text: Yes, after a run has finished the `sequence_n.pdb` files will be 500 in number and correspond to the 500 structures in `ensemble.n.pdb`. Other ensemble files contain structures from previous iterations.
Answers.UserDisplayName: jgreener
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-15T08:39:02.130Z
Answers.Text: I noticed a behavior of the program I have: I left "run_dmpfold.sh" to run for two days without touching the system using the command line I mentioned, at that time dmpfold had produced  "sequence_71.pdb" file, and after 2 days when I check, there were no more number pdb files than "sequence_71.pdb". When I logged into the system as it was on sleep mode, the number of "sequence_71.pdb" stared increasing to "sequence_72.pdb"..etc. Hence, actually 2 days were lost where dmpfold was not producing files. Can you please let me know why this might have happened?
Answers.UserDisplayName: DanielSebas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-16T09:25:21.873Z
Answers.Text: It sounds like your machine went to sleep, which will have paused all running processes. This isn't a DMPfold issue, it's more an OS issue. Have a look at tools like https://mac-how-to.gadgethacks.com/how-to/take-control-your-macs-sleep-functions-with-these-commands-0168109/ to sort this out.
Answers.UserDisplayName: jgreener
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-16T11:52:51.023Z
Answers.Text: yes, I corrected it by "aborting suspend" in my system settings. Thanks
Answers.UserDisplayName: DanielSebas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-16T16:34:17.687Z
Answers.Text: Another query to clarify, I see that after generating "sequence_n.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"? I mean when can I expect "final_1.pdb' file? Also, I see files like "CLUSTERS_001.pdb". thanks!
Answers.UserDisplayName: DanielSebas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-17T09:29:04.230Z
Answers.Text: 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.
Answers.UserDisplayName: jgreener
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-12T15:38:06.527Z
Answers.LastActivityDate: 2019-09-12T15:38:06.527Z
Answers.UserDisplayName: jgreener
Body: <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>
  
Tags: <protein-structure>
Title: DMPfold: Understand the run of DMPfold "run_dmpfold.sh"?
ThreadText: # DMPfold: Understand the run of DMPfold "run_dmpfold.sh"?
  
  (Asked by: username_0 on 2019-09-12)
  
  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.
  
  **Tags:** protein-structure
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-09-12. Score: 1 | Accepted answer
  
  From the [docs](https://github.com/psipred/DMPfold):
  
  > 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!
  
  > **Comments:**
  > **username_0**: Just one question: "output files before clustering" and "ensemble files": are these also 500 + 500 in number?  
  > **username_1**: Yes, after a run has finished the `sequence_n.pdb` files will be 500 in number and correspond to the 500 structures in `ensemble.n.pdb`. Other ensemble files contain structures from previous iterations.  
  > **username_0**: I noticed a behavior of the program I have: I left "run_dmpfold.sh" to run for two days without touching the system using the command line I mentioned, at that time dmpfold had produced  "sequence_71.pdb" file, and after 2 days when I check, there were no more number pdb files than "sequence_71.pdb". When I logged into the system as it was on sleep mode, the number of "sequence_71.pdb" stared increasing to "sequence_72.pdb"..etc. Hence, actually 2 days were lost where dmpfold was not producing files. Can you please let me know why this might have happened?  
  > **username_1**: It sounds like your machine went to sleep, which will have paused all running processes. This isn't a DMPfold issue, it's more an OS issue. Have a look at tools like https://mac-how-to.gadgethacks.com/how-to/take-control-your-macs-sleep-functions-with-these-commands-0168109/ to sort this out.  
  > **username_0**: yes, I corrected it by "aborting suspend" in my system settings. Thanks  
  > **username_0**: Another query to clarify, I see that after generating "sequence_n.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"? I mean when can I expect "final_1.pdb' file? Also, I see files like "CLUSTERS_001.pdb". thanks!  
  > **username_1**: 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.  
  
  ---
  
  