How to export defocus value for each micrographs

CTF Estimation
1

Hi,

I’d like to ask a simple question that how to export defocus value of each image after CTF for plotting?

2

Welcome @jiangl!

You can download a csv table from the interactive GUI of Manually Curate Exposures job type.

Best,
Kookjoo

3

Thanks! I tried with Manually Curate Exposures. But I have a further question that is how to export defocus value on X and Y axis that are shown as DF1 and DF2 on diagnostics figure produced by patch CTF estimation job. The table from Manually Curate Exposures shows the average defocus value.

4

One way I can think of is converting the exposures_ctf_estimated.cs from Patch CTF to a star file via csparc2star.py in pyem. Include the passthrough.cs file along with your exposures.cs to have micrograph filenames in the output star.

From the converted star file, you can extract _rlnDefocusU and _rlnDefocusV for each micrograph.

Best,
Kookjoo

1 Like
5

Yes, csparc2star.py works for micrographs as well.

Note the two defocus values are not on X and Y, but the major and minor axes of the ellipse with major axis rotated by the given angle.

1 Like
6

@jiangl To avoid confusion, please can you post the figure to which your question refers.