Can this be done after the job has run? I am not seeing an invert/zflip option in the 3dvar job or display and volume tools invert hand gives an error. I guess each output volume from the series could be manually z-flipped prior to opening as a series as a last resort.
Unfortunately this is not supported right now directly from cryoSPARC, but yes you can manually flip all the volumes that come out in the series. We will add this option.
Wouldn’t it be easier to flip the input parameters? E.g. flip the reference and re-run refinement using the volume tools. There’s no particle parameter hand flip in cryoSPARC I think, but there is in
star.py from pyem.
@DanielAsarnow is right - probably it is easier to just re-run refinement from a flipped input reference, then re-run 3DVAR after that