Particle off center


I have particle of ~130kDa that compose from Fab and antigen. After blob picking and 2D class the COM is on the Fab and not the full particle (see image). Is there a way to shift the centering so to full particle will be center?


Unfortunately not in cryoSPARC (assuming the particles were picked off center). Your best bet is to generate a centered reconstruction and then re-extract in RELION with recentering.

In order to generate centered 2D classes, you can try switching on the “recenter mask binary” option and adjusting the threshold, but as cryosparc does not use offsets to recenter particles upon re-extraction there is not really any point.


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@Elad Extract From Micrographs will now re-center particles by default if they have already been extracted and aligned through 2D classification, 3D reconstruction, or refinement (v.3.0+)