[phenixbb] phenix.refine : mask

Pavel Afonine pafonine at lbl.gov
Thu Oct 7 01:03:49 PDT 2010


>> 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.

yes, currently this is the only way to do this in PHENIX.


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