Patch-based CTF

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#1

Where can I get more information about the meaning of plots in the new patch-based CTF job (2.8.0)? Thanks.
PS: I misspoke when I asked about motion correction. That’s clear, but the green vertical lines and ice-thickness plots in patch-based CTF aren’t quite clear. Thanks.


#2

Hi @rbehrouzi, please see this post for more information on Patch CTF.


#3

Thanks @spunjani , but there’s no mention of the relative ice thickness plot and what to read from it, which I couldn’t understand!


#4

Hi Reza,

I am guessing here, but looking at the “relative ice thickness” parameter it seems very similar to the “iciness” parameter introduced in Focus (https://www.biorxiv.org/content/biorxiv/early/2017/03/17/105452.full.pdf), and also IIRC from twitter discussions possibly being implemented in the next version of CTFFIND - @spunjani, can you confirm?

Cheers
Oli


#5

Also - if I can add an additional question - what is the meaning of “knots” in the context of Patch CTF and Patch Motion? In context, it seems to mean patches - e.g. Patch CTF defaults to 3 knots in X and 3 in Y - is this more or less correct or is there a more specific meaning? I notice that Patch Motion defaults to 5 knots in Z - does this mean it is using a rolling window of 5 frames and interpolating shifts for the frames within that window?

Cheers
Oli


#6

One more thing - unless I’m missing it, the “relative ice thickness” parameter doesn’t seem to be plottable in the exposure curation job.

This might be a useful parameter to have here, to allow users to easily test the exclusion of icy data.

Cheers
Oli