I used both homogeneous and non-uniform refinement to refine a map with about 110 000 particles. I reach a final resolution of 2.8 / 2.9 A. At the center of the map, I always see a sphere in the density that seems to correspond to nothing when the protein is modeled inside> I wonder if it could be a processing artefact and how it should be handled.
Thank you,
Hi @fbontems,
Can you confirm the symmetry that was enforced - C3? D3?
And did you see this central density only in non-uniform refinement, or also in homogeneous refinement?
We do sometimes see some artefactual density appearing along the symmetry axis for highly symmetric particles, but usually the density is much lower than protein density elsewhere in the map.
You’re absolutely sure this is not part of the molecule?
Hi Apunjani,
Thank you for your answer. I observe this density whatever I do (no symmetry, C3 symmetry, homogeneous and non-uniform refinement, with and without static masks).When I was young, one of my teachers used to say « when you find something unexpected, it is either a small discovery or a huge mistake, and in most of the cases, it’s a huge mistake ». This density corresponds to nothing expected in the protein we analyse, Then before claiming I observed something unexpected, I prefer to be sure that it can not be an artefact. The fact that makes me very suspicious is that the density is perfectly spherical and exactly at the center of the map.
Thank you again,
François Bontems