I’m not sure what the practical result of turning off bulk-solvent correction in Phenix is, but it’s almost always a bad idea. The affected reflections are low-resolution and thus usually high-amplitude, and messing with these can have a huge effect on map quality. (This is one reason why overloads are bad.) Phenix calculates the mask automatically; I’m not sure what CNS does, but the image above implies that it needs separate input. It’s been so long since I’ve used CNS that I can’t remember what I used to do for this procedure (I modified the scripts by hand, anyway), but I never used separate mask files. Omit maps are always noisier, but for a well-refined structure, the CNS composite omit map usually won’t disagree with the maps from refinement.

Warm welcome!

If your map is nearly traceable then it sounds like you are on the right track. Thanks for the reference on Iterative omit maps – good read.

I had a question about when you set the bulk solvent correction to false… will the result in your omit map be very noisy density between NCS mates?

The reason I ask is because I performed a simple sigma weighted omit map via phenix on a troublesome structure, and the resulting map gave me very “inflated” density, and the areas around the different chains that make up my structure were very noisy, what looks to be solvent. However I was excited because the omit map appears to be traceable to some extent.

One last thing, I did start a run on a iterative composite omit map after reading Terwilliger et al paper:
Iterative build OMIT maps: Map improvement by iterative
model-building and refinement without model bias

Hopefully this will result in a more interpretable map.