Hi,
While doing ab initio reconstruction I find that for one of the model views there is a circular smear like a Halo in the background. I haven’t seen that before. Do you have any idea of what that might be? And if there is a way to avoid it? I attach a pic for reference.
Thanks a lot!
Samara
Not sure if it is the reason, but it looks like your box is too small for the particle - your particle is brushing up against the edge of the soft circular mask.
Thanks @olibclarke for your reply. I am working with a complex that is around 115A, the pixel size is 0.825. I am using a box size of 256 px. How much do you think should I increase it? For 2D classes, I am using a mask of 180A. Do you think that should also be changed? Thanks a lot for your insights!
Best,
Samara
Hi Samara,
From your ab initio it seems the particle might be a little bigger than that?
Measuring the longest dimension of your particle from the slices of your ab initio (and comparing to your box size), it looks like ~160Å, which is a bit too large for your box size (211 Å).
I would suggest trying a box size of 384px, ~double your particle size, as a starting point. 320px might also be ok for initial classification, but I think 256px is a bit too small for your particle.
Cheers
Oli
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Thanks a lot @olibclarke will try that 
Also for considering what box size to choose, think about CTF delocalization, see this snippet from Rosenthal & Henderson 2003 which is very useful in that regard:
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