CryoSPARC Guide

Job: Global CTF Refinement

Per-group beam tilt, trefoil, spherical aberration, tetrafoil.


Global CTF Refinement performs per-exposure-group CTF parameter refinement of higher-order aberrations, against a given 3D reference structure. Read a tutorial here.


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


  • Particle set with updated CTF parameters

Common Parameters

  • Number of iterations: controls the number of iterations of CTF refinement that are done. It is important that the number of iterations is at least 2 when anisotropic magnification is being estimated together with the other aberrations. This is to allow the aberrations to be fit to the data while accounting for anisotropic magnification. If only aberrations are being estimated, 1 iteration is usually sufficient.
  • Minimum fit res (A): controls the minimum resolution used for fitting. Generally global CTF refinement should be done only with medium to high resolution signal, as low resolution signal can be unreliable. 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.
  • Fit Tilt/Trefoil/Spherical Aberration/Tetrafoil: Select which higher-order aberrations should be refined. Tilt and Trefoil are 3rd order aberrations and require less high resolution signal to accurately detect, compared to spherical aberration and tetrafoil which are 4th order. In some cases, optimizing the 4th order terms can be detrimental, especially if per-particle defocus or the 3rd order terms are not yet correctly refined. Note: as of v4.0, only the third-order aberrations (Tilt and Trefoil) are fit by default, whereas the fourth-order aberrations (Spherical Aberration and Tetrafoil) are not fit by default.
  • Fit Anisotropic Magnification: Activate to enable the estimation of anisotropic magnification. Note that this is inactive by default, since significant anisotropic magnification is a relatively rare phenomenon compared to beam tilt and other aberrations. When turning on this option, be sure to set the Number of iterations to at least two.