PT  - JOURNAL ARTICLE
AU  - Fang-Chieh Chou
AU  - Nathaniel Echols
AU  - Thomas C. Terwilliger
AU  - Rhiju Das
TI  - RNA Structure Refinement using the ERRASER-Phenix pipeline
AID  - 10.1101/001461
DP  - 2013 Jan 01
TA  - bioRxiv
PG  - 001461
4099  - http://biorxiv.org/content/early/2013/12/19/001461.short
4100  - http://biorxiv.org/content/early/2013/12/19/001461.full
AB  - 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).