CryoSPARC Guide

Job: Local CTF Refinement

Per-particle defocus.


Local CTF Refinement performs per-particle defocus estimation for each particle in a dataset, against a given 3D reference structure. Read a tutorial here.


  • Particles
    • ctf (required)
    • alignments3D (required)
    • blob (required)
  • Volume
    • map (optional)
    • map_half_A (required)
    • map_half_B (required)
    • mask_refine (optional)
  • Mask
    • mask (optional)


  • Particle set with updated CTF parameters

Common Parameters

  • Minimum fit res (A): controls the minimum resolution used for fitting. Generally CTF refinement should be done only with medium to high resolution signal, as low resolution signal can throw off CTF fits. For smaller particles, change this to a higher resolution.
  • Maximum fit res (A): controls the maximum resolution used for fitting. Higher resolution signal is better for CTF refinement, until there is too much noise present in the half-maps. Leave this blank to have the maximum resolution automatically determined via FSC between the two input half-maps.
  • Defocus search range: controls how far above and below the current defocus to search for the optimal defocus of each particle. If you used Patch CTF Estimation previously in cryoSPARC, this value can be made relatively small, about the same as the thickness of ice you expect to have in the sample, since the input defocus values will already be fairly accurate.