Ilan E Chemmama

Added a test pdb here with figures to show the shift observed. Left panel show the model and the generated map when opened in Chimera and the right panel shows...

What do you mean by offset? Resolution-wise or coordinate-wise?

**Update 1:** - Difference in box is because constructor (ii) based its box size on the header while constructor (iii) based its box size on the particles passed. - Changing...

**Update 2**: - To fix constructor (ii), the origin needs to be updated before adding particles, _e.g._: ``` sampled_input_density = IMP.em.SampledDensityMap(mrc.get_header()) sampled_input_density.set_origin(p2d_mrc.get_origin()) sampled_input_density.set_particles(ps) sampled_input_density.resample() sampled_input_density.calcRMS() ``` Just need to compute...

**Update 3**: - Work around that seems to be working but need further testing: Aligning the centroid of the model with the centroid of the bounding box seems to have...

I have seen it happened before; it is one of the reason I do not rely on `CoarseCC` anymore and developed the new scoring function. When I saw the behavior,...

Seeing a behavior that may be related: `CoarseCC.cross_correlation_coefficient` for near optimal localization is most always negative. (ccc < 0.).