after I make Ab-initial with my negtivestain data in cryosparc, I get a weired model like this, which show extra density specifically in X-Y axis.
though I can remove this by changing threshold, I’m still wondering why this heppened, because in my previous job using the same setting with cryo-data, my model didn’t have these extra data.
thanks a lot if you can solve this question
Hi @J6H55! This looks to me like it may be ringing or some other Fourier artifact. I wouldn’t worry too much about it in this case, since the magnitude is relatively small.
Incidentally, it looks from this slice like your box size is much larger than your particle – you may see significant speed improvements if you extract with a smaller box size, especially since negative stain data does not have significant delocalized signal from the CTF.
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my box is indeed larger, because particle is super motivative.
thanks a lot!!!