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Kabsch
Dan,
I'm not sure what you're asking. But, if I'm correct both interpreting what you're thinking and the math, then yes. To do so, just append the CB list to the CA list for each protein respectively and align.
If you have CA and CB from two proteins, you can align all CAs to CAs and all CBs to CBs. All you have to do is to figure out how to tell the alg to do it.
This should do the trick:
optAlign proteinA and ((n. CA and i. 4+5+10+22) or (n. CB and i. 5+10+15+20)), proteinB and ((n. CA and i. 1-4)or (n. CB and i. 30+31+35+49))
If it works, let me know -- drop off an image or something. GL.