Angpix and box size change after reconstruction of negative stain data

3D Reconstruction
1

Hello everyone,

I’m processing negative stain data on cryosparc and have noted that the box size and angpix reported in chimeraX from my downloaded ab initio and homogenous refinement jobs don’t match my extraction box size and/or the angpix I specified when I imported my micrographs.

My maps should have box size 100 and angpix 1.51, but ChimeraX reports them as box size 64 angpix 2.36 even though I never did any fourier cropping on my particles. In a different workspace an ab initio had a box size of 128 and angpix of 1.61 while the homogenous refinement built from that job has box size 140 and angpix 1.51.

I’m not sure what’s causing this issue and would appreciate your thoughts.

Best regards,

Andre

2

CryoSPARC automatically downsamples during both ab initio and heterogeneous refinement for speed. It doesn’t sample back. If you want to get back to the original box size, do a quick homogeneous reconstruction for the map. :slight_smile:

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