text: user16933: i have two protein pdb files and want to calculate the backchain RMSD between them. As far as I know the GUI of Pymol can use align to calculate the RMSD (but I don't know if it is the backchain RMSD).I want to use the python code to use pymol to calculate the backchain RMSD. I know how to align them but don't know how to calculate the RMSD.
  import pymol2
  with pymol2.PYMOL() as pymol:
      pymol.cmd.load('foo.pdb', 'foo')
      pymol.cmd.load('bar.pdb', 'bar')
      pymol.cmd.align('foo', 'bar')
      
  
  
  user6322: The backbone can be specified using a selector for the names of these, which are N, CA (Cα) and C (C-prime).
  out = pymol.cmd.align('foo and name N+CA+C and polymer', 'bar and name N+CA+C and polymer')
  rmsd, n_atoms, n_cyles, n_rmsd_pre, n_atom_pre, score, n_res = out
  
  If you do not wish the proteins to be moved you can use rms_cur, which is just the rmsd.
  
original_text: 16933: <p>i have two protein pdb files and want to calculate the backchain RMSD between them. As far as I know the GUI of Pymol can use align to calculate the RMSD (but I don't know if it is the backchain RMSD).I want to use the python code to use pymol to calculate the backchain RMSD. I know how to align them but don't know how to calculate the RMSD.</p>
  <pre><code>import pymol2
  with pymol2.PYMOL() as pymol:
      pymol.cmd.load('foo.pdb', 'foo')
      pymol.cmd.load('bar.pdb', 'bar')
      pymol.cmd.align('foo', 'bar')
      
  </code></pre>
   6322: <p>The backbone can be specified using a selector for the names of these, which are <code>N</code>, <code>CA</code> (Cα) and <code>C</code> (C-prime).</p>
  <pre><code>out = pymol.cmd.align('foo and name N+CA+C and polymer', 'bar and name N+CA+C and polymer')
  rmsd, n_atoms, n_cyles, n_rmsd_pre, n_atom_pre, score, n_res = out
  </code></pre>
  <p>If you do not wish the proteins to be moved you can use <code>rms_cur</code>, which is just the rmsd.</p>
  