code: public static final List<Chain> getAlignedModel(Atom[] ca){
  
  		List<Chain> model = new ArrayList<Chain>();
  		for ( Atom a: ca){
  
  			Group g = a.getGroup();
  			Chain parentC = g.getChain();
  
  			Chain newChain = null;
  			for ( Chain c :  model) {
  				if ( c.getId().equals(parentC.getId())){
  					newChain = c;
  					break;
  				}
  			}
  			if ( newChain == null){
  
  				newChain = new ChainImpl();
  
  				newChain.setId(parentC.getId());
  
  				model.add(newChain);
  			}
  
  			newChain.addGroup(g);
  
  		}
  
  		return model;
  	}
docs: get an artificial List of chains containing the Atoms and groups.
  Does NOT rotate anything.
  @param ca
  @return a list of Chains that is built up from the Atoms in the ca array
  @throws StructureException