How is the solvent mask handled for zero occupancy atoms? In general is it justified that i fear some of the electron density belonging to the protein in the periphery of the molecule can be solvent flattened and i never see them thereafter in my electron density maps or is this just not going to happen (i.e., the density for protein will never be averaged out)?
I have a 1.97A dataset for a ~570 odd residue protein with two domains that had independently been solved earlier. My phaser solution had most of the residues fit in density for the full length protein but i am in the process of building the residues that were absent in the search models and there are some trouble areas that i set to zero occupancy and did a simulated annealing refinement in phenix . (Is this the omit map that will point to general features in the region that i had set to zero occupancy?)
This from phenix documentation:
mask
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