[phenixbb] Refinement with partial model - question
PAfonine at lbl.gov
Thu Apr 1 08:23:57 PDT 2010
> 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
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