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

Pavel Afonine pafonine at lbl.gov
Sat Apr 20 20:45:45 PDT 2013

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? 


> 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,

More information about the phenixbb mailing list