Fundamental flaw on particle locations

[apunjani]

Hi @alburse,

Presuming you are using @DanielAsarnow’s great pyem tools for conversion?
Please check out this post for some discussion about x/y conventions.

Bayesian Polishing of cryosparc-processed particles

Hi all, Thanks @DanielAsarnow and @olibclarke for clarifications. CryoSPARC Patch Motion does in fact write out motion trajectories (as plain numpy array files in the job output dir) but Relion or other programs will not know how to read these. Also the reason for the --swapxy (I believe - looking through pyem code) is that in cryoSPARC, we use the convention that 2D/3D arrays are always stored in C-order, with the fastest axis being the “x” axis, and we use a right hand coordinate system. Tha…