Answers.Body: <p>RMSD is a measure of similarity between two structures. The relevant RMSD in protein structure prediction is between a model and the native structure. If you don't have a native structure you cannot have an RMSD in this sense. Ignore the fact it is 0.0, there is possibly some error that means you are calculating the RMSD between a model and itself.</p>
  
  <p>And that's the difficulty of protein structure prediction... you don't know whether you are right or not! The structures you have generated are your results, and you'll need to find ways to filter or use them that are not reliant on RMSD. You could use estimation of model accuracy methods or clustering, for example.</p>
  
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Answers.CreationDate: 2019-09-23T15:09:27.107Z
Answers.Text: thanks, when following the tutorial:https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction; it says " However, if no related structure is known, you would use e.g. the lowest energy model (and rescore the top models with e.g. -native best_E.pdb)." Can you let me know how can I "rescore" the models? Thanks
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Answers.CreationDate: 2019-09-23T15:04:26.883Z
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Answers.UserDisplayName: jgreener
Body: <p>I am running rosetta ab initio prediction using the command line:</p>
  
  <pre><code>"mpiexec -np 16 /main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database /main/database/ @options -mpi_tracer_to_file log &gt; log1.log &amp;"
  </code></pre>
  
  <p>"Options" file looks like this: <a href="https://ibb.co/V9VrQHV" rel="nofollow noreferrer">https://ibb.co/V9VrQHV</a></p>
  
  <p>RMSD vs Energy plot is:
  <a href="https://ibb.co/1mjzwDj" rel="nofollow noreferrer">https://ibb.co/1mjzwDj</a></p>
  
  <p>There is no native structure as this is an ab initio prediction. Could you please let me know about your comments on the RMSD being 0.00 for all 2000 models generated till now? Is this normal and will produce results after more runs? </p>
  
Tags: <protein-structure>
Title: Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)
ThreadText: # Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)
  
  (Asked by: username_0 on 2019-09-23)
  
  I am running rosetta ab initio prediction using the command line:
  
  ```
  "mpiexec -np 16 /main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database /main/database/ @options -mpi_tracer_to_file log > log1.log &"
  
  ```
  
  "Options" file looks like this: <https://ibb.co/V9VrQHV>
  
  RMSD vs Energy plot is:
  <https://ibb.co/1mjzwDj>
  
  There is no native structure as this is an ab initio prediction. Could you please let me know about your comments on the RMSD being 0.00 for all 2000 models generated till now? Is this normal and will produce results after more runs?
  
  **Tags:** protein-structure
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-09-23. Score: 1
  
  RMSD is a measure of similarity between two structures. The relevant RMSD in protein structure prediction is between a model and the native structure. If you don't have a native structure you cannot have an RMSD in this sense. Ignore the fact it is 0.0, there is possibly some error that means you are calculating the RMSD between a model and itself.
  
  And that's the difficulty of protein structure prediction... you don't know whether you are right or not! The structures you have generated are your results, and you'll need to find ways to filter or use them that are not reliant on RMSD. You could use estimation of model accuracy methods or clustering, for example.
  
  > **Comments:**
  > **username_0**: thanks, when following the tutorial:https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction; it says " However, if no related structure is known, you would use e.g. the lowest energy model (and rescore the top models with e.g. -native best_E.pdb)." Can you let me know how can I "rescore" the models? Thanks  
  
  ---
  
  