RNA Structure Refinement Using the ERRASER-Phenix Pipeline

  • Fang-Chieh Chou
  • Nathaniel Echols
  • Thomas C. Terwilliger
  • Rhiju Das
Part of the Methods in Molecular Biology book series (MIMB, volume 1320)


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).

Key words

RNA structure Structure prediction X-ray crystallography Refinement Force field 



The authors would like to thank Sergey Lyskov for implementing and maintaining the ROSIE Rosetta server, and members of the Rosetta and the Phenix communities for discussions and code sharing. The authors acknowledge support from Howard Hughes International Student Research Fellowship (F.C.), Stanford BioX graduate student fellowship (F.C.), Burroughs-Wellcome Career Award at Scientific Interface (R.D.), NIH grants R21 GM102716 (R.D.) and P01 GM063210 (P.D. Adams, PI, to N.E. and T.T.).


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Fang-Chieh Chou
    • 1
  • Nathaniel Echols
    • 2
  • Thomas C. Terwilliger
    • 3
  • Rhiju Das
    • 1
  1. 1.Department of BiochemistryStanford UniversityStanfordUSA
  2. 2.Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  3. 3.Bioscience DivisionLos Alamos National LaboratoryLos AlamosUSA

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