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I need to manually build a model in Coot without a map. I want to link to 2 loops from 2 DNA strands together by base-pairings while keep the rest part as freezing as possible. The sequences of the loops are complimentary but the current orientations of the loops is not correct. Is there a way to add restraint between the loops to force them base-pairing while keep the rest part of the 2 DNA strands fixed? 

Another question is how to measure the angles between two DNA helices? I have seen a command to measure protein helices in PYMOL but did not find one for DNA helices.

Thanks for your great help!

Cheers,

Frank