# RNA Structure Refinement using the ERRASER-Phenix pipeline

## TL;DR

This paper introduces a pipeline that improves RNA structure modeling by combining two computational methods, making RNA crystallography more efficient and accurate.

## Contribution

The novel contribution is the ERRASER-Phenix pipeline, which integrates Rosetta-based and diffraction-based refinement for RNA structure refinement.

## Key findings

- The ERRASER-Phenix pipeline improves RNA model geometry while maintaining or enhancing fit to diffraction data.
- The pipeline is accessible through multiple interfaces including GUI, command-line, and the ROSIE server.

## Abstract

The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatically based on a physically realistic model of atomic-level RNA interactions. The pipeline couples diffraction-based refinement in Phenix with the Rosetta-based real-space refinement protocol ERRASER (Enumerative Real-Space Refinement ASsisted by Electron density under Rosetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fit to the diffraction data (as measured by Rfree). Here we present a complete tutorial for running ERRASER-Phenix through the Phenix GUI, from the command-line, and via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).