Re: [phenixbb] dummy atom v.s. model with zero occupancy.

Hi Lithlin,

In phenix, in order to improve bulk solvent model when the model is not complete, you can add dummy atom and set "refinement.mask.ignore_zero_occupancy_atoms=False".

correct. This will not let bulk-solvent into that area and therefore it will make missing bits more visible.

My question is that can I just put a model ( I know the approximate position for the model) there instead of dummy atoms and set all atoms in the model zero occupancy and keep the same setting.

Will I get the same result?

Yes.

I suspect that model will still be used to calculate the Fc even though the occupancy is zero, so the map will be severely model biased.

Sorry, I understood this part.. All the best, Pavel