Hi,
> I'm using a very tight mask for 2d classification because my particles are packed together in the micrograph. I wonder though if I can switch to a
> bigger mask diameter for 3d classification and 3d refinement.
To some extent yes, but too large values can make refinement slower,
because it means finer angular sampling for a given resolution,
and refinement less accurate, because of noise from neigboring particles.
> Lastly, I read that box size matters for proper ctf estimation and defous refinement,
For initial CTF estimation (in CTFFIND), not really. It does not use high resolution
and the box is big (512 px @ 1.4 A/px by default) anyway.
For high resolution refinement and CTFRefine, yes.
> but does the particle mask itself matter during any step of the processing?
No. The 2D circular mask is not applied to backprojection (reconstruction)
in Refine3D/Class3D. CTFRefine also does not use the value (it does not know the value).
Best regards,
Takanori Nakane
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