Recentering classes on extraction?

hi all

is there a way to recenter particles on extraction? I have a long tube-shaped protein with larger mass on the end (like a hammer). However often my averages end up with the handle of the hammer in the center, while I want the head of the hammer.

In relion it is possible to re-extract particles given an X/Y/Z shift, but is this possible in cryosparc? A handy tool would be where you can open up your 2D averages and click each avg to set a new position for extraction, then use that as input for an extraction. Maybe it’s excessive, I dunno.


I think that would be a wonderful tool to be able to define the recenter of the class averages before re-extraction. :smiley:

this would be great!

just to be sure… is there absolutely any way to recenter your particles in cryosparc?

I did a refinement and used the output particles from that to re-extract from the micrographs (hoping it would carry over the X/Y shift and other metadata). But the newly extracted particles still look extremely off-center when I follow by a 2D run. I suppose it’s possible I just have tons of incorrectly assigned angles in my initial recon…

if it is NOT possible to recenter then this could be a fundamental problem, as signal near the edge of the box may experience aliasing (particularly if the box is not big enough).


It should recenter on extraction according to the offsets associated with the particles (e.g. from 2D classification or 3D refinement), but there is no way to recenter on an arbitrary X.Y to my knowledge (as you described in your initial post).

If it isn’t recentering according to the offsets from refinement I would consider that a bug.


@orangeboomerang @olibclarke
CryoSPARC currently does not recentre particles on extraction but we do plan to implement this in a future version.

Really?? Well that is good to know I had been assuming that it did… that is unfortunate