Continuous heterogeneity is often well modelled by 3D Variability components, as the first examples in this tutorial demonstrate. In the default
simple mode, cryoSPARC's
3D Variability Display job will create a volume series using the consensus refinement and the 3D Variability component itself to show how the 3D structure changes. This results in a series that contains a smoothly varying, linear change in 3D density values from one end of the series to the other. This linear approximation is often very good for showing small detailed motions and conformational changes within the protein structure, but it can break down for larger motions. In those cases, it can be helpful to construct a volume series by reconstructing separate volumes directly from subsets of the particle images, sorted and chosen by their reaction coordinate value. This technique, of sub-sampling a dataset in the latent space (i.e., reaction coordinates) for visualization, has been used by other methods that involve representing particles in a reaction coordinate space. These reconstructions are called
intermediate reconstructions in cryoSPARC, and can be created using the
3D Variability Display job in
intermediate mode. In this mode, particles are sorted along each variability dimension, and then split into (overlapping) subsets, weighted by their position along the variability dimension. This creates a "rolling window" of particles selected for creating each intermediate reconstruction in a volume series.