Before revision: RNA crystallographic models contain pervasive ambiguities due to the difficulty of manually fitting RNA backbones into experimental density maps . Recent advances in ab initio RNA structure prediction suggest an automated way to resolve these ambiguities. We present a protocol for Enumerative Real-space Refinement ASsisted by Electron density under Rosetta (ERRASER), coupled to PHENIX diffraction-based refinement.
After revision: Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density under Rosetta (ERRASER), coupled to PHENIX diffraction-based refinement.