Superimposing structure pieces

I've been trying to pull out pieces of protein chains and superimpose
them...my current code (as generic-ified code snips below) works, but
I wonder if it couldn't be faster.
Has anyone worked on similar methods?  Any other advice?

Best regards everyone,
da

Getting residue CA's as Atom[]:

for (int i; i < length; i++) {
    someAtoms[i] = someChain.getSeqResGroup(start + i).getAtom("CA");
}

Superimposing/aligning:

SVDSuperimposer svds = new SVDSuperimposer(someAtoms1, someAtoms2);
Matrix rot = svds.getRotation();
Atom trans = svds.getTranslation();
for (int i = 0; i < length; i++) {
    Calc.rotate(someAtoms1[i], rot);
    Calc.shift(someAtoms1[i], trans);
}
SVDSuperimposer.getRmsd(someAtoms1, someAtoms2);
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