Exporting particles after aligning movies in cryosparc


I patch aligned in CS then exporting to re-extract in relion on externally-aligned Motioncor2 movies. I think CS flips images or something because my gain flip/rot is always different between the two.

Anyways I can’t get the picks to match up with the MC2 mics. I tried Csparc2star with and without --swap_xy. Is there some other rotation/flip going on that I’m unaware of?

please… create an export tool…