Hi,
I’ve noticed that when refinement of per particle scale is switched on, the minima in the defocus error landscape during local CTF refinement are a lot shallower (and presumably less accurate?). Is this expected? And if so, is it recommended to first refine per particle defocus, then minimize over per particle scale?
Hi @olibclarke,
Thanks for bringing this to our attention – we’ve triaged it as something to investigate, and may reply with a request for more details. For now, is this something you’ve noticed once-off, or has it been consistently the case that the defocus error minima are much shallower after scale-refinement is done?
Best,
Michael
Once off but I’ve only tested it once, I haven’t had an extensive look
There is definitely some interplay between per particle scale & defocus. For example, in another case, here are the per-particle scale factors before per particle defocus:
And here are the per-particle scale factors after per particle defocus refinement:
This makes me think that it’s at least plausible that scale refinement may compensate for local defocus differences (which may cause issues with identifying the correct per-particle defocus values).
