code: public void align(Structure s1, String chainId1, Structure s2,
  			String chainId2, StrucAligParameters params)
  			throws StructureException {
  		reset();
  		this.params = params;
  
  		Chain c1 = s1.getPolyChainByPDB(chainId1);
  		Chain c2 = s2.getPolyChainByPDB(chainId2);
  
  		Structure s3 = new StructureImpl();
  		s3.addChain(c1);
  
  		Structure s4 = new StructureImpl();
  		s4.addChain(c2);
  
  		Atom[] ca1 = getAlignmentAtoms(s3);
  		Atom[] ca2 = getAlignmentAtoms(s4);
  
  		notifyStartingAlignment(s1.getName(), ca1, s2.getName(), ca2);
  		align(ca1, ca2, params);
  	}
docs: Aligns two chains from the structures using user provided parameters.
  
  @param s1
  @param chainId1
  @param s2
  @param chainId2
  @param params
  @throws StructureException