On Sat, Sep 15, 2012 at 1:19 PM, Pavel Afonine
Yes, that's the trick. We should streamline it somehow.
It's not clear to me why that parameter is True - in what other circumstances would we expect to find zero-occupancy atoms? A related question: what happens in phenix.maps when omit.selection is set? Right now, it looks like this simply deletes the selected scatterers from the xray structure object, which I assume means the bulk solvent mask will expand to fill the gap. Wouldn't a better method be to set the occupancies to zero and not ignore them when calculating the mask?
However, removing such a big fraction of atoms at once can't be painless: you can't remove arbitrarily large amount of atoms and expect a useful map after that. May be you should split atoms to omit into fractions (like 1/3 or so), and compute OMIT maps for each one fraction, and then combine resulting maps into one.
It's only about 1/8th of the structure (although those phosphates will contribute a lot), so it shouldn't be too awful. But at this resolution I'm not sure what to expect. -Nat