Single particle cryo-EM tools

We offer single particle cryo-EM software for analyzing stacks of extracted particles. At the moment, we do not offer end-to-end single particle analysis (motion correction through to final 3D refinements).

Currently available tools

  • RELION-v3.1
    • ISAC (iterative stable alignment & classification): performs 2D classification on particle stacks to recover rare states
  • cryoDRGN – deep learning-based analysis of protein conformational landscapes
  • DeepEMhancer – map modification to sharpen 3D reconstructions
  • Local map interrogation/modification
    • LocSpiral – Sharpen map using spiral phase transform
    • LocBfactor – Estimate and sharpen maps with local B-factors
    • LocOccupancy – estimate occupancy of a region in 3D reconstruction
  • Conversion software
    • csparc2star – convert cryoSPARC .cs file to .star format for RELION
  • Efficiency – measure the distribution of particle orientations in a 3D reconstruction
  • Align Projections – align reprojections of 3D reconstruction with 2D class averages

Tools organized by job purpose

  • 2D classification
  • 3D classification
    • RELION
  • 3D refinement for high-resolution
    • RELION
  • 3D flexibility analysis 
    • RELION Multibody, cryoDRGN
  • Map modification
    • DeepEMhancer, LocSpiral, LocBfactor, LocOccupancy
  • Validation
    • Efficiency, Align Projections
  • Conversion
    • csparc2star

Questions? Email