Hi Sjors,
you are right, I did not have the ctffind3 log files in the micrographs directory when I extracted the frames. When extracting, I used micrographs_ctf.star file as input, and that one did have all the defocus and microscope parameters. I assumed that relion would take CTF values from there rather than going to Micrographs/*.log files.
Thanks,
Klim
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