Per particle scale and per particle defocus?

CTF Refinement
1

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?

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2 Likes
2

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

3

Once off but I’ve only tested it once, I haven’t had an extensive look

4

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:

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And here are the per-particle scale factors after per particle defocus refinement:

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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).

5

Hello! Wanted to bump this to ask if there’s a recommended good practice to follow given the differences noted in local CTF estimation depending on adjustments to the per particle scale. It’s been a couple years since this discussion, but I couldn’t find any more information on this otherwise. Thank you!