CryoSPARC Guide

Job: 3D Variability Display

3D variability display.


  • Create various versions of a 3D variability result that can be used for display. Read a tutorial here.


  • Particles (from 3D Variability Analysis)
  • Volume (from 3D Variability Analysis)

Common Parameters

  • Output mode: simple mode: output a simple linear "movie" of volumes along each dimension. Number of frames is the next param. cluster mode: fit clusters to reaction coordinates and output volumes and particles from each cluster. Number of clusters is the next param. intermediates mode - reconstruct multiple intermediate volumes along each variability dimension, useful for better visualizing non-linear changes. Number of intermediate frames is the next param. endpoints mode - split particles in two parts along each dimension and reconstruct, useful for creating initial volumes for classification/hetero refinement. Always two outputs per dimension.


  • A series of frames for each component of the variability detected in the dataset, each as a .zip file
  • Learn more about running 3D Variability Display and viewing an interactive 3D scatter plot, in this tutorial.

Common Next Steps

  • Visualization of results through UCSF Chimera or similar.