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    Rhiju says:

    For G*U wobble pairs, you can use STEM PAIR; it is considered a Watson-Crick pair by the code.

    We haven’t included cis/trans classifications yet, because the code authors find antiparallel/parallel more intuitive and robust from a modeling perspective. Given a set of interacting base edges, there is a mapping from cis/trans to parallel/antiparallel, however, and allowing cis/trans input would be a good feature for future updates of Rosetta.