text: user12686: I have 3884 PDB files generated by 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) or Scaleable Molecular Dynamics (NAMD) *?
  Can anyone tell me what command I should use in console mode?
  * note, this server may be unavailable
  
  user6717: You can use 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
  
  
original_text: 12686: <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>
   6717: <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>
  