Hey @co-cool,
Thanks for the question. In the Extract from Micrographs jobs, the Fourier crop to box size parameter allows you to decreasing the particles’ box size by increasing their pixel size. The final box size of the extracted particles is the value set in this parameter. Reducing the box size is typically done to speed-up downstream processing during early phases of processing a dataset, because nearly all processing will run significantly faster at smaller box sizes.
For example, if your micrographs have a raw pixel size of 0.5 Å and you instead want the extracted particles to have a pixel size of 1.0 Å, you can set the Fourier crop to box size (pix) parameter to half the value of the Extraction box size (pix) parameter.
By increasing the pixel size, the sampling rate of the images is decreased, and thus higher frequency information is lost during the Fourier crop operation. The effect this has on resolution depends on whether your dataset has enough SNR (and homogeneity, etc.) to reach the Nyquist resolution in the first place. If you expect a final resolution of x Å, you are safe to Fourier crop particles to a pixel size of at most (x/2) Å without adverse affects. It’s quite common to do initial processing at a smaller box size, and after an initial structure is obtained, to go back and repeat the process at a larger box size only if the Nyquist resolution limit is hit.
Best,
Michael