code: public Structure getAlignedStructure(Structure s1, Structure s2){
  		// do not change the original coords ..
  		Structure s3 = s2.clone();
  
  		currentRotMatrix.print(3,3);
  
  		Calc.rotate(s3, currentRotMatrix);
  		Calc.shift( s3, currentTranMatrix);
  
  		Structure newpdb = new StructureImpl();
  		newpdb.setPDBCode("Java");
  		newpdb.setName("Aligned with BioJava");
  
  
  		newpdb.addModel(s1.getChains(0));
  		newpdb.addModel(s3.getChains(0));
  
  		return newpdb;
  
  	}
docs: create an artifical Structure object that contains the two
  structures superimposed onto each other. Each structure is in a separate model.
  Model 1 is structure 1 and Model 2 is structure 2.
  
  @param s1 the first structure. its coordinates will not be changed
  @param s2 the second structure, it will be cloned and the cloned coordinates will be rotated according to the alignment results.
  @return composite structure containing the 2 aligned structures as a models 1 and 2