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*
......
