I have a query regarding the new patch-based CTF estimation algorithm. Based on the 3D-surface that is generated, it looks like the algorithm has some kind of local smoothing - assuming that nearby regions have similar defocus values.
This will be more or less true for particles in thin ice that is bent or tilted, but is unlikely to be true for large particles in thick ice, where often a lot of the variation in per particle defocus comes from the z-position of the particle in the ice (e.g. adhered to one interface vs the other), rather than the shape of the ice itself. In this case it is quite common that two particles adjacent in x-y will have very different z-positions, and hence different local defocus values.
Is there any plan to take account of this, e.g. by refining the patch based estimates at the extracted particle positions during the Patch CTF Extract job, or as another parameter to refine during homogeneous refinement?