After Ewald sphere correction in either non uniform or homogeneous refinement, it ought to be possible to estimate the local mean defocus at a given point in the volume (e.g. as per the “block-based” reconstruction method described here: Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions | Nature Communications).
Would it be possible to optionally allow Volume Alignment tools to modify per-particle defocus values accordingly? This would be helpful when performing refinement of subparticles (e.g. refining a portal in the capsid of a virus, for example).
Thanks for the interesting request! It would be possible to adjust the defocus based on a desired local position in the volume (center of mass of the subparticle?), together with the initial defocus and the known particle orientation. Volume alignment tools would make sense to do this since it functions as a subparticle selector. It’s on our radar, likely we would want to experiment a bit with this to see in which cases it makes the biggest differences, most likely large viruses If I’m thinking about it right, it wouldn’t even need Ewald sphere correction as a precursor; it only depends on good alignments and good initial defocus estimates (which we would presume to represent the defocus of the true center of the particle).
DeRosier 2000 provides an explanation of the claim that Ewald sphere curvature and local defocus variation within a sample can be viewed as equivalent problems, although admittedly the full understanding of why this is true isn’t grasped very well by our team yet…
It would be possible to adjust the defocus based on a desired local position in the volume (center of mass of the subparticle?), together with the initial defocus and the known particle orientation.
Yes exactly! This is done by localrec as implemented in Scipion, see section 3.1.1 here: Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data - ScienceDirect
I see, thank you for the literature reference for localrec!