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

Jinzhong Lin jzlsci at gmail.com
Sat Apr 20 19:40:22 PDT 2013


Dear PHENIX users,

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".

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.

Lithlin


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