EMRinger: Side Chain-Directed Model and Map Validation for 3D Cryo-Electron Microscopy

Nat Methods. 2015 Oct;12(10):943-6. doi: 10.1038/nmeth.3541. Epub 2015 Aug 17.

Abstract

Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cryoelectron Microscopy / methods*
  • Crystallography, X-Ray
  • Databases, Protein
  • Image Processing, Computer-Assisted / methods*
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry*
  • Reproducibility of Results
  • Software*
  • TRPV Cation Channels / chemistry

Substances

  • Proteins
  • TRPV Cation Channels
  • Trpv1 protein, rat

Associated data

  • PDB/3J9I
  • PDB/3J9J