[phenixbb] phenix.refine : mask

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Wed Oct 6 17:51:40 PDT 2010

Hi Bryan,

> i gather that the only way to define an "a priori" mask of the molecular  
>envelope in phenix.refine is to generate Fmask and combine those in refinement -  
>is that right?
> i.e. there isn't a more intuitive way using a mama mask or  somesuch to keep 
>the bulk
> solvent from flattening out parts you think are model,  besides the model that 
>is being
> refined in the first  place?

Nothing elegant, but with mask.ignore_zero_occupancy_atoms=False
and adding zero-occupancy atoms to the pdb file you can get the
desired effect. I've never tried it, though. You probably need to
pack the atoms quite closely and add selections to keep them fixed.


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