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

Pavel Afonine pafonine at lbl.gov
Sun Apr 21 08:54:40 PDT 2013

As a P.S.:

I would be interested to see how this looks like. So if you send me the 
data and model and all else necessary to reproduce this and explain how 
to reproduce this I would greatly appreciate it.


On 4/20/13 7:40 PM, Jinzhong Lin wrote:
> 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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