title: Aligning 2 small molecules in PyMOL
body: <p>I want to align to ligands in PyMOL like one would do it with protein structures, but I get an error message:</p>
  
  <p><code>ExecutiveAlign: mobile selection must derive from one object only</code></p>
  
  <p>I also copied the ligands into separate PDB files, renamed the <code>HETATM</code> entries to <code>ATOM</code>, but still I get this error. I am wondering why PyMOL has problems aligning those small molecules.</p>
  
  <p>PS: Those ligands have similar structure, only different coordinates.</p>