Can anyone help me interpret these plots:
These are the outputs of running CTF estimation job.
Hi @Ashwin-Dhakal! Let me try to explain these plots a bit for you.
The first plot is used to assess the fitted envelope function. It plots the fitted CTF, the power spectrum, and the envelope. I discussed it a bit in another forum post.
The second plot should show you the relative ice thickness, like this one:
In these plots we measure the background strength (black line) in the region where thicker ice increases background (blue fill) and call that the “relative ice thickness”.
The last two plots show you information the fitted 2D CTF. On the right is the power spectrum of the micrograph, and on the left is the fitted 2D CTF. The blue surface plot shows you the fitted defocus for each position along the micrograph. The x- and y-coordinates correspond to the coordinates of the micrograph, and z corresponds to the defocus.
These plots don’t look quite right — can you confirm that all four came from the same micrograph? I’d like to try help figure out what’s going wrong during your CTF estimation.
1 Like
I would guess it is after motion correction with motioncor2 instead of Patch Motion? In my experience something about the difference in background estimation between the two throws off the relative ice thickness measure and also results in non-visible Thon rings in the 2D power spectrum plot
Interesting!! How curious!
It was reported here, but as far as I am aware not fixed yet: Thon rings not showing up in exposure curation
Thanks @olibclarke for pointing out the likely cause - noted!
@Ashwin-Dhakal to confirm, were your micrographs coming from motioncor2 rather than patch motion?