Answers.Body: <p>You can use <a href="https://www.cgl.ucsf.edu/chimera/" rel="nofollow noreferrer">Chimera</a> for this. The following code cleans your pdb file and write new pdb file.</p>
  <pre><code>import chimera
  from DockPrep import prep
  from chimera import runCommand, openModels
  
  models = chimera.openModels.list(modelTypes=[chimera.Molecule])
  prep(models)
  runCommand(&quot;write format pdb 0 molecule.pdb&quot;)
  </code></pre>
  <p>You can run the code with</p>
  <pre><code> chimera --nogui file.pdb code.py
  </code></pre>
  
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Answers.Text: how do I get chimera ?  pip install pychimera https://pypi.org/project/pychimera/ ??? is there a python3 version ?
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Answers.Text: https://pychimera.readthedocs.io/en/latest/ --> Use UCSF Chimera packages in any Python 2.7 interpreter
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Body: <p>I have 3884 PDB files generated by <a href="http://www.sbg.bio.ic.ac.uk/%7Ephyre2/PD2_ca2main/" rel="nofollow noreferrer">pd2_ca2main</a>. PD2 CA2main is server for reconstructing the backbone of Calpha proteins using Gaussian mixture models.</p>
  <p>All of these files have duplicate atoms or alternate coordinates.</p>
  <p>How can I clean these PDB files using Visual Molecular Dynamics (<a href="https://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/01-vmd-tutorial/html/node2.html" rel="nofollow noreferrer">VMD</a>) or Scaleable Molecular Dynamics (NAMD) <strong>*</strong>?</p>
  <p>Can anyone tell me what command I should use in console mode?</p>
  <p><strong>*</strong> note, this server may be unavailable</p>
  
Tags: <protein-structure><pdb><protein-protein-interaction>
Title: How can I clean a PDB file using VMD or NAMD?
ThreadText: # How can I clean a PDB file using VMD or NAMD?
  
  (Asked by: username_0 on 2022-10-25)
  
  I have 3884 PDB files generated by [pd2\_ca2main](http://www.sbg.bio.ic.ac.uk/%7Ephyre2/PD2_ca2main/). PD2 CA2main is server for reconstructing the backbone of Calpha proteins using Gaussian mixture models.
  
  All of these files have duplicate atoms or alternate coordinates.
  
  How can I clean these PDB files using Visual Molecular Dynamics ([VMD](https://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/01-vmd-tutorial/html/node2.html)) or Scaleable Molecular Dynamics (NAMD) **\***?
  
  Can anyone tell me what command I should use in console mode?
  
  **\*** note, this server may be unavailable
  
  **Tags:** protein-structure, pdb, protein-protein-interaction
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-11-13. Score: 1
  
  You can use [Chimera](https://www.cgl.ucsf.edu/chimera/) for this. The following code cleans your pdb file and write new pdb file.
  
  ```
  import chimera
  from DockPrep import prep
  from chimera import runCommand, openModels
  
  models = chimera.openModels.list(modelTypes=[chimera.Molecule])
  prep(models)
  runCommand("write format pdb 0 molecule.pdb")
  
  ```
  
  You can run the code with
  
  ```
   chimera --nogui file.pdb code.py
  
  ```
  
  > **Comments:**
  > **username_2**: how do I get chimera ?  pip install pychimera https://pypi.org/project/pychimera/ ??? is there a python3 version ?  
  > **username_1**: https://www.cgl.ucsf.edu/chimera/download.html  
  > **username_2**: https://pychimera.readthedocs.io/en/latest/ --> Use UCSF Chimera packages in any Python 2.7 interpreter  
  
  ---
  
  