CEAlign > 0 for exact same structures ?

Hi guys.. Im finding that two structures that are the same give me non-zero
RMSD alignments....   There could be a bug in my code, but this is an
initial notice that I'm pretty sure about.... Any thoughts on the
performance of CEAlign in ideal cases ?


        Atom[] ca1 = GPdbUtils.getAtoms(s1, type);
        Atom[] ca2 = GPdbUtils.getAtoms(s2, type);

        System.out.println("Aligning two sets of atoms, " + ca1.length
+","+ca2.length);
        // get default parameters
        CeParameters params = new CeParameters();

        // set the maximum gap size to unlimited
        // params.setMaxGapSize(-1);
        StructureAlignment algorithm = StructureAlignmentFactory
                .getAlgorithm(CeMain.algorithmName);

        // The results are stored in an AFPChain object
        AFPChain afpChain = algorithm.align(ca1, ca2, params);
        afpChain.setName1("A");
        afpChain.setName2("B");

        return (float) afpChain.getChainRmsd();
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