How to specify boxsize in Ab reconstruction?

Hello, everyone! I have imported particle stack into cryoSPARC with box size 256 and run 2D classification jobs with specific mask diameter. I found that there were noise around the edge of my target region after checking the results of Ab reconstruction. So I wonder how to specify a smaller box size during reconstruction without re-extracting particles? Thanks a lot.

Hi @Verdandy,

While it isn’t possible to manually specify the numeric box size used by ab-initio (the box size is determined implicitly through the Maximum resolution (Angstroms) parameter), it sounds like you are trying to crop your images in real-space, rather than perform Fourier-space downsampling. This could help if your initial extraction box size was too big, and includes too much noise in the edge/corners of the box, as you remarked.

This can be done in CryoSPARC v4.1+ by using the “Downsample Particles” job. You can input the particles to the job, and then set both the Crop to box size (pix) and Fourier crop to box size (pix) to the same value, which should be less than your current box size of 256. This will crop the particles in real-space to this value without any additional Fourier-space downsampling. Hence, the pixel size of the images will stay the same, and it will just crop out the box edges more tightly.


Thanks Michael ! I have tried Downsample Particles job following your suggestion. And It came out with perfect results. Thanks a lot.

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