A starting point for phenix.refine it would be nice to restrain the sugar puckers, the planarity of the bases (themselves), and the planarity of WC base pairs and the distances between them (the implementation in CNS). A useful machine readable format that the user can use for this is the dot-bracket notation (http://rna.tbi.univie.ac.at/help.html#A6) and the inclusion of the brackets ( [ ] ) for pseudoknots. The user specifies the dot bracket notation and the sequence and its easy to write the secondary structure (essentially establishing all the base pairs).
Thanks for the suggestions, that's very helpful moving forward. Phenix.refine currently does have restraints for both 3' and 2' sugar pucker, as well as pucker-specific backbone restraints. Each sugar pucker is determined automatically, and the proper restraints applied. Nat and I are currently working on how to restraint WC base pairs as a start, so hopefully that will be included very soon. Thanks for the suggestions on how to allow user input, I'll take a closer look at these links as we move along. Take care, Jeff