Hi @apunjani and @DanielAsarnow
To follow on this question, we calibrated the apix of our microscope and I don’t think the apix is off. Therefore could this be due to any other reason?
For example, on this website (https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Pixel_size_issues), it shows that when apix is off you will have a strange bump in the FSC curve, while my FSC curve does not look like that.
Actually, @DanielAsarnow mentioned in another thread (How to refine pixel size?) that this type of FSC looks like a membrane protein dip. Can you elaborate more on that or suggest some references for reading?
Back to the spherical aberration question, on that website (https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Pixel_size_issues) it was also mentioned that SphericalAberration will remain the same while the error in Cs is expressed in EvenZernike. Does cryosparc also has a similar parameter? For example here is my final refined parameters.
[CPU: 10.21 GB] Phase shift (rad): -0.0299637569282
[CPU: 10.21 GB] Delta-DF1 (A): 6.95718088903
[CPU: 10.21 GB] Delta-DF2 (A): 6.31573571901
[CPU: 10.21 GB] Delta-Ast (rad): 1.19080749641
[CPU: 10.21 GB] Spherical Aberration (mm): [ 3.58319371]
[CPU: 10.21 GB] Tetrafoil (A): [-135002.18093295 -137469.02652034 623149.91276625 199063.79591239]
Again thank you for teaching me all these. Any suggestion or comment will be highly appreciated.