Using CTFFIND with movies

I am about to start processing my first data set collected as movies on a Falcon II using RELION and CTFFIND. When used together with RELION, the general approach seems to be to run CTFFIND on the average of all frames. However, I was wondering whether it is possible in CTFFIND to calculate a power spectrum from each frame separately, average these together and then estimate the CTF? I suspect in some cases, especially with very long exposures, this approach would give more accurate CTF estimates.

CTFFIND3 can only read in one image, unfortunately. So what you are trying to do cannot be done with CTFFIND3.