Hi there,
I’m trying to solve a amyloid filament structure. I am confused, do I need to use a box size in the extract from micrographs job that is big enough to contain a whole crossover segment of the filament? (It is rather long, something about 670A-s)
Or is there a way to extract with 300-400pixel big boxes and then create the whole map from those data?
It takes ages with big box 
Hi @kiaract,
If you extract at a larger box size, you can always downsample (eg 600 → 300 px) to help get a clean particle stack and then you could extract at full size for your final refinements. Here is a publication where CryoSPARC was used to determine the structure of an amyloid fibril and might be a good reference for you to follow: https://www.pnas.org/doi/10.1073/pnas.2406775121
Cheers,
Kye