Patch-based CTF



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.


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


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


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 (, and also IIRC from twitter discussions possibly being implemented in the next version of CTFFIND - @spunjani, can you confirm?



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?



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.



@olibclarke did you ever get an answer to this question? I am also curious too!


Not yet! But I would still be curious to know the answer too


Hi @olibclarke @ekellogg,

Relative ice thickness is similar to what is done in Focus - measuring the amount of power in the ice resolution band relative to the overall background.
The overall background unfortunately is highly sample/scope/setup dependant, making it hard to compare rel. ice thickness values across datasets. Within a dataset it’s pretty good for separating thin from thick ice. Thanks for pointing out that ice thickness is missing from exposure curation - we will add this.

Knots in patch motion and CTF are not actually patch sizes - generally more patches are used than the number of knots. The knots are parameters of the spatial and temporal smoothing - more knots means more degrees of freedom in each dimension.