I’m trying to estimate local per-particle ctfs using the gctf wrapper and a set of micrographs with associated particles (either extracted directly or with local motion correction). Whereas it seems to work for a couple of micrographs and the program runs for a while, the ctf fit and defocus values reported seem to be stuck at what I imagine are one of the parameter extremes.The issue seems to persist even when I input global ctf values.
I’m attaching snaphsots of my input parameters and of the output. Notice how most ctf fit values are stuck at 1.84A and the average defocus at 89800A.
Please let me know if there is any other information I can provide towards identifying the issue.