In some cases ab initio can assign Rodrigues vectors of (0,0,0) - are these particles ignored by cryoSPARC or it’s just an identity rotation? Thanks!
In our exponential map implementation, (0,0,0) does map to the identity rotation so it is a possible value for refined poses. However, we do also initialize
alignments3D/pose to (0,0,0) so if you are seeing numbers exactly equal to 0, then these are almost certainly unprocessed particles (perhaps from ab-initio?).
Thanks, that makes sense. I was just thinking about what to do with them, after correcting my the csparc2star.py code to output an identity rotation for those particles (so at least it doesn’t crash for the user). Folks shouldn’t really be using those angles for anything anyway, so I’m just going to leave it how it is now.
(There is a rlnEnabled field that can be used to ignore particles as well but I don’t want to inject more complexity for users).