code: public static StructureAlignmentJmol display(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException {
  
  		if ( ca1.length < 1 || ca2.length < 1){
  			throw new StructureException("length of atoms arrays is too short! " + ca1.length + "," + ca2.length);
  		}
  
  		Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain, ca1, ca2);
  
  		List<Group> hetatms  = StructureTools.getUnalignedGroups(ca1);
  		List<Group> hetatms2 = StructureTools.getUnalignedGroups(ca2);
  
  		return DisplayAFP.display(afpChain, twistedGroups, ca1, ca2, hetatms, hetatms2);
  
  	}
docs: Display an AFPChain alignment
  
  @param afpChain
  @param ca1
  @param ca2
  @return a StructureAlignmentJmol instance
  @throws StructureException