Need help understanding patch ctf estimation output files

CTF Estimation
1

CTF patch estimation for a micrograph outputs three files

  1. ctf_spline.npy (shape 1,5,5)
  2. ctf_diag_plt.npy
  3. ctf_diag_2D.mrc (shape 768,768,1)

I would like to compute df1 and df2 for a certain coordinate of the micrograph (e.g. 500,500)
Could you help me understand how to do that?

Thanks in advance,
Andreas

2

Hi @azamanos! I think the easiest way to do this would be to use cryosparc-tools to generate a dataset which has a particle in the position(s) you desire on the micrograph(s) you want to inspect, then use Patch CTF Extraction to calculate the CTF at those positions.

3

Hi, I am coming from another thread where you linked me here. Could I get a slightly more detailed explanation for generating a dataset with particle positions on the micrographs that I have already done patch ctf for? I think I have to append to the existing cs file but I have no previous experience with the API

4

Hi @fjkoh, no problem. I’ve written up in a bit more detail how you might go about creating a particle dataset and extracting CTF values with cryosparc tools here. I hope that’s helpful!

5

Thanks a ton! It is extremely helpful.

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6

I’m trying to understand the tilt of the micrographs, is the df_tilt_normal value relating to the physical tilt of the image (alpha tilt and alpha tilt axis) or the astigmatism of the image?

7

Hi @fjkoh! df_tilt_normal is the angle between the normal vector of the defocus surface and vertical. You can think of this as, essentially, *half of the stage tilt.

*Currently half the stage tilt, see @olibclarke’s note below (thank you!)

8

It should correspond to the stage tilt - but at present (depending on upstream processing) it is often half the stage tilt, for reasons that are still not entirely clear to me: Curious Tilt angle in patch CTF - #19 by rbs_sci

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