I’m working with a tetrameric ion channel. After NUR (res 4.10) I did C4 sym expansion followed by local refinement (res 3.7) to model a single protomer of the channel, as the NUR volume quality was lacking in the TMD and the peripheral regions of the protein. I built the best possible model I could with the map and according to Phenix (CCmask: 0.72) and the PDB validation tool statistics.
To build the NUR C4 map, I took the protomer, copied it four times, and docked it into the NUR C4 map. After very minor tweaking in ISOLDE to get the chains into the exact right positions I ran RSR in phenix and overall have a good model (99% rama favored, no rotamer outliers, good CaBLAM etc) but the CCmask has gone down to 0.66, and RCSB validation shows Q scores per chain of around ~0.285.
This makes sense to me. Portions of the NUR map that are not resolved well (like blobs or amorphous shapes) or are lacking in density are going to impact CC and Q scores. The local refine map has great contouring of sheets and helices, whereas the NUR map doesn’t always have these in the poorly resolved regions (hence the need for a focused local refinement).
My initial thought was I needed to rectify this by deleting sidechains that are not in density, or even remove the small segments (sometimes up to 5+ amino acids) of chains that don’t seem to be in an appropriate density. I don’t have a lot of problematic areas, so it’s not a difficult exercise. However, after looking at some other models of similar channels in the PDB, I see this isn’t necessarily done. I’ve found several examples where there are focused refinements of the deficient areas, but the full map+model have models that are built into no density or problematic density.
I don’t know if there is a consensus on what to do in these situations, and I can see the very valid pros and cons of each option investigators choose to do. Composite maps also seem available, but with lots of strong opinions in the field.
Does one just build a full model using the well reconstructed and validated protomer, and ignore the deficiencies of NUR map? Or should you try and make the protomer model match the map and fix deficient segments through pruning and removal?