Bin pix size and box size

Cryo-EM Data Processing
1

Dear experts,

As a newcomer to cryo-EM processing, I’d be grateful for your guidance on a basic question about CryoSPARC:

When refining particles that were initially extracted from bin4 data but now working in bin1, do we need to adjust both the pixel size and box size of the reference map that was generated from the bin4 particles?

I understand this adjustment is required in RELION (using relion_image_handler), but I’m unsure:

  1. If CryoSPARC has the same requirement
  2. Where exactly such adjustments should be made in the workflow if needed

Apologies！

2

In CryoSPARC it is not necessary to adjust the size of the reference.

It’s also not necessary in RELION 5 (if the appropriate option is set) but the RELION rescale can pass through slight errors in pixel size if using “odd” scaling/cropping factors, although that can be overcome with --force_header_angpix XYZ…

1 Like
3

Thanks a ton! This helps me a lot！