title: Align & save structure segment only
body: <p>I am trying to align a short segment within structure A to a short structure B.
  I tried following <a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/protein_superposition/" rel="nofollow">"Protein Superposition using Biopython"</a></p>
  
  <p>But because I only want to a short segment from A and save this one, I am getting problems saving the results.</p>
  
  <p>Calling alignment works fine:</p>
  
  <pre><code>super_imposer.set_atoms(residuesBCA,residuesACA)
  </code></pre>
  
  <p>and the consecutive transformation to the alignment position runs through</p>
  
  <pre><code>for residue in residuesACA:
      residue.transform(super_imposer.rotran[0],super_imposer.rotran[1])
  </code></pre>
  
  <p>but I cannot check the result because I cannot save the residues with</p>
  
  <pre><code>io = PDBIO()  
  io.set_structure(residuesACA)
  io.save('./' + pdbFile)
  </code></pre>
  
  <p><code>io</code> here expects a full structure, but in the previous loop I only transformed the segment residues. How can I save them to disk?</p>