Ask for help for enlongated particles in 2D classfication or particle picking

2D Classification
1

hi, all

My protein has a much more enlongated (50X50X300) and stick-like shape, it looks like a filament but without symmetry. I used the general procedures for particle picking and 2D classification in cryoSPARC. As a result, it indeed showed as a filament-like shape in 2D. However, it seems bad in finding the right center so that a large part of classes look shorter with just centering on one head. No improment when I simply adjusted the mask and re-center threholds.
Do you anyone have some expreriences and suggestions for such a kind of enlongated-shape particles?
Thanks a lot!

best,
Niu

2

Hi Niu,

I recommend trying Topaz for particle picking. You can use the Cryosparc integration of Topaz to do this (also denoising if you need help seeing your particles in the micrographs). I recommend manually picks for curating several dozen micrographs or more (make sure the particle picks are centered well), then training a model. After training, use an extaction radius in Topaz Extract that is large enough to not give duplicate picks.

Let me know if this works or not.

Best,
Alex Noble