Not directly related to the use of cryosparc, but would be happy to hear if someone has good experience with the density modification (resolvecryoEM) of phenix.
I think the result is not too dissimilar to that of sharpening, or of using deepEMenhancer. I think the low resolution features will be largely gone.
I see that in this paper is used after NU refinement/local refinement, with quite a bit of gain in resolution (whatever that means in terms of real gain in quality of the map) https://www.nature.com/articles/s41592-020-01021-2.pdf
(by the way, quite interesting what they did with cryosparc on sorting 2D classes).
I think it is a great tool to squeeze out a little extra information from your reconstructions to help modeling. Maybe Iâm too conservative, but personally I wouldnât take the results for deposition or use the determined FSC as resolution estimate.
Especially in less resolved regions (by flexibility, heterogeneity etc.) local resolution will drop making the âsharpeningâ suffer and artificial.
Also, sharpening of structures with very heterogeneous electron scattering like ribosomes (rna vs protein) seems not to work well.
I agree mostly with tarek, although I believe itâs fine to deposit the density modified map as long as thatâs what you used to build/refine and you also deposit the associated half-maps used as input, and donât report phenix-resolve resolution. I agree it can oversharpen, but it can also brings out really nice improvements. Like many things, itâs highly dependent on local resolution.
If my pixel size is 2Ă /pixel (super resolution on K3 is 1Ă /pixel), is it possible to push the resolution beyond the Nyquist (4Ă ) by processing the super-resolution images directly (without binning=2)? Anybody had the experience? Thanks!
(But still possible!)