code: public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) throws StructureException{
  
  		/* Previous implementation commented
  
  		Structure s = new StructureImpl();
  
  
  		List<Chain>model1 = getAlignedModel(ca1);
  		List<Chain>model2 = getAlignedModel(ca2);
  		s.addModel(model1);
  		s.addModel(model2);
  
  		return s;*/
  
  		Structure s = new StructureImpl();
  
  		List<Chain>model1 = getAlignedModel(ca1);
  		s.addModel(model1);
  		List<Chain> model2 = getAlignedModel(ca2);
  		s.addModel(model2);
  
  		return s;
  	}
docs: Get an artifical Structure containing both chains.
  Does NOT rotate anything
  @param ca1
  @param ca2
  @return a structure object containing two models, one for each set of Atoms.
  @throws StructureException