[phenixbb] Defining planarity for Phenix.refine

Jeff Headd jjheadd at lbl.gov
Mon Apr 19 19:23:27 PDT 2010

> 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,

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