pafonine at lbl.gov
Sat Sep 15 13:19:15 PDT 2012
>> 1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part)
>> from pdb and ran phenix.refine with simulated_annealing=True. But resulted
>> Fo-Fc in the omitted region is very weak. Is it because of the low
>> resolution and because big part of the model was omitted?
> This is part of the problem - another possible contributing factor is
> that the bulk solvent mask will extend into the DNA site, which
> flattens out the difference density. An alternate way to do this
> (which should work) is to set the occupancy of the DNA to zero, which
> will remove any contribution to the scattering, and set the parameter
> ignore_zero_occupancy_atoms=False, which will prevent the mask from
> extending into the DNA.
Yes, that's the trick. We should streamline it somehow.
However, removing such a big fraction of atoms at once can't be
painless: you can't remove arbitrarily large amount of atoms and expect
a useful map after that. May be you should split atoms to omit into
fractions (like 1/3 or so), and compute OMIT maps for each one fraction,
and then combine resulting maps into one.
More information about the phenixbb