Dear all,
I have two datasets of the same protein sample collected on two different dates 13 days apart with the same microscope and settings (apix, dose).
I processed the data on CryoSPARCv4.2.1 in two separate workspaces from motioncorr to 3d refinement before trying to merge the two sets of particles. Both sets of particles (same box size) were exported and reimported to match the pixel size (prior error mismatch in pixel size up to 4 decimal places).
However the 2D classes seem to show opposite data sign (screenshot 1 below). I tried “minimize over per particle scale” during 3D refinement (screenshot 2 below) and “Min over scale after first iteration” for 2D classification, both approaches did not seem to help in correcting the scale difference (assuming if this is the root issue).
I am very puzzled and hope to seek any insights please on how to fix this and what I had done wrongly.
