Answers.Body: <p>This is described briefly in <a href="https://www.nature.com/articles/s41467-019-11994-0" rel="nofollow noreferrer">the paper</a>. The four quantities are inputs to the estimator of model accuracy:</p>
  
  <ul>
  <li><code>nres</code> is the sequence length.</li>
  <li><code>neff</code> is an effective sequence count, or how deep the alignment was.</li>
  <li><code>dpscore</code> is how well the final model matches the initial distance prediction.</li>
  <li><code>dpscorenorm</code> is a normalised version of the above.</li>
  </ul>
  
  <p>Don't worry too much about directly interpreting these. They are only given for completion. The important line is <code>Estimated TM-score of ../final_1.pdb is 0.5</code>, indicating that DMPfold just about thinks this is a decent model.</p>
  
  <p>The "sequence.ema.txt" is more raw output giving the probability of the TM-score being in each bin. "rawdistpred.1" is the distance predictions from the first iteration. Always use "rawdistpred.1" as input to the TM-score predictor as this is how it was trained.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-24T10:24:26.753Z
Answers.LastActivityDate: 2019-09-24T10:24:26.753Z
Answers.UserDisplayName: jgreener
Body: <p>So, my runs have finished and got 5 final models. I predicted TM-score of one model to understand the result. The output of "predict-tmscore.sh" for "final_1.pdb" is:</p>
  
  <pre><code>1 models read from PDB file
  1 models read from PDB file
  nres is 377
  neff is 15423
  dpscore is -300.599030
  dpscorenorm is -0.082424
  Probability of each TM-score bin (cols 1-10), estimated TM-score (col 11) and prob TM &gt; 0.5 (col 12) written to sequence.ema.txt
  Estimated TM-score of ../final_1.pdb is 0.5
  </code></pre>
  
  <p>could you please help me understand what does "nres", "neff", "dpscore", and "dpscorenorm" below mean: </p>
  
  <pre><code>    nres is 377 
  neff is 15423 
  dpscore is -300.599030 
  dpscorenorm is    -0.082424
  </code></pre>
  
  <p>and it also generates a "sequence.ema.txt" file with below value:</p>
  
  <pre><code>2.0308916646172293e-05 2.0682286958617624e-06 0.04564645141363144 0.14857041835784912 0.27177685499191284 0.31814685463905334 0.19150513410568237 0.022412151098251343 0.001872337656095624 4.743059980683029e-05 0.5036169363265117 0.5339840054512024
  </code></pre>
  
  <p>Please let me know what these above values signify?</p>
  
  <p>And,I would really appreciate your comments on what does "rawdistpred.1" file mean? There are total 9 such files. When predicitng TM-score, do I need to use "rawdistpred.1" file for all final models or I can use any "rawdistpred.*" file? </p>
  
  <p>thanks!   </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-24T10:50:51.647Z
Comments.Text: Excellent question and answers on two core structure prediction programs
Comments.UserDisplayName: M__
Tags: <protein-structure>
Title: What does final generated models with TM-score of DMPfold signify in "sequence.ema.txt" file?
ThreadText: # What does final generated models with TM-score of DMPfold signify in "sequence.ema.txt" file?
  
  (Asked by: username_0 on 2019-09-24)
  
  So, my runs have finished and got 5 final models. I predicted TM-score of one model to understand the result. The output of "predict-tmscore.sh" for "final\_1.pdb" is:
  
  ```
  1 models read from PDB file
  1 models read from PDB file
  nres is 377
  neff is 15423
  dpscore is -300.599030
  dpscorenorm is -0.082424
  Probability of each TM-score bin (cols 1-10), estimated TM-score (col 11) and prob TM > 0.5 (col 12) written to sequence.ema.txt
  Estimated TM-score of ../final_1.pdb is 0.5
  
  ```
  
  could you please help me understand what does "nres", "neff", "dpscore", and "dpscorenorm" below mean:
  
  ```
      nres is 377 
  neff is 15423 
  dpscore is -300.599030 
  dpscorenorm is    -0.082424
  
  ```
  
  and it also generates a "sequence.ema.txt" file with below value:
  
  ```
  2.0308916646172293e-05 2.0682286958617624e-06 0.04564645141363144 0.14857041835784912 0.27177685499191284 0.31814685463905334 0.19150513410568237 0.022412151098251343 0.001872337656095624 4.743059980683029e-05 0.5036169363265117 0.5339840054512024
  
  ```
  
  Please let me know what these above values signify?
  
  And,I would really appreciate your comments on what does "rawdistpred.1" file mean? There are total 9 such files. When predicitng TM-score, do I need to use "rawdistpred.1" file for all final models or I can use any "rawdistpred.\*" file?
  
  thanks!
  
  **Tags:** protein-structure
  
  > **Comments:**
  > **username_1**: Excellent question and answers on two core structure prediction programs  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-09-24. Score: 2 | Accepted answer
  
  This is described briefly in [the paper](https://www.nature.com/articles/s41467-019-11994-0). The four quantities are inputs to the estimator of model accuracy:
  
  * `nres` is the sequence length.
  * `neff` is an effective sequence count, or how deep the alignment was.
  * `dpscore` is how well the final model matches the initial distance prediction.
  * `dpscorenorm` is a normalised version of the above.
  
  Don't worry too much about directly interpreting these. They are only given for completion. The important line is `Estimated TM-score of ../final_1.pdb is 0.5`, indicating that DMPfold just about thinks this is a decent model.
  
  The "sequence.ema.txt" is more raw output giving the probability of the TM-score being in each bin. "rawdistpred.1" is the distance predictions from the first iteration. Always use "rawdistpred.1" as input to the TM-score predictor as this is how it was trained.
  
  
  ---
  
  