[phenixbb] Refinement with partial model - question

[Pavel Afonine]

Hi Peter,

> I have a partial model at low resolution.  Is there a way  let 
> Phenix.refine know the model is not complete and that when a mask is 
> calculated for bulk solvent correction it should take this fact into 
> consideration ?

No. Bulk solvent mask is set up everywhere where there is no model. May 
be it is a reasonable approximation at early stage of refinement to have 
something in that area than vacuum?

> Alternatively, is there a program that will build dummy atoms (zero 
> occupancy) automatically in a map in all peaks above a certain sigma 
> (i.e. atoms just for mask calculation).

I'm not aware of such program although it's a couple of hours to write 
one. I would probably even write it if I ever see a clear need for it or 
evidence for its usefulness. So far I don't understand why you really 
need it?

Pavel.