Potential bug in heterogenous refinement when using larger window inner radius

During 3D refinement jobs (heterogenous, homogenous, NU, local), I have to use a larger window inner radius (0.95 instead of 0.85) to avoid masking of my map at one end. I noticed that in heterogenous refinement only (but not in homogenous, NU, and local ref.) the larger window inner radius is in effect only at the final iteration. I.e. when looking at the real space slices for intermediate iterations, my map is still masked at one end.

On a related note, can someone explain how cryosparc handles image/map recentering?



Hi @Yazan,
Sorry for the delay - thanks for reporting this.
During a refinement, the map is not re-centered since we start with an initial volume and it is assumed that the initial model is well centered. During ab-initio reconstruction, re-centering does occur. Particles are never re-centered explicitly, but the search range for shifts is generally quite wide so it doesn’t usually matter.