Re: [phenixbb] phenix.refine : mask

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. Ralf