On Mon, May 17, 2010 at 10:53 AM, xaravich ivan
So I have quite a few regions build by the SA_omit map of phenix. But How do I go about looking at these maps. What am I looking for here. Should I look at the regions where the occupancy was set zero in all these outputs and find if I could build some thing from one of the maps? I guess I am asking, How do I use this information to move forward in refinement? There are 24 regions map and .pdb output in the /OMIT directory.
Ignore these - only the final map is useful. If you are generating a composite omit map, you want to make sure that what you've built still matches the density reasonably well. Obvious things to look at: - flexible or missing loops - ligands - anywhere the mFo-DFc map shows large blobs at +/- 3sigma - any outliers flagged by validation (both geometry and real-space correlation) I don't usually find it productive to go through the structure residue-by-residue, but this may depend on the data and model quality. What is your resolution and current R-free? (If you are just omitting part of the structure, then you only need to look at the map around those atoms - the rest won't be much different.) -Nat