[phenixbb] Sa_Omit_map_DNA_low_resolution

Nathaniel Echols nechols at lbl.gov
Sat Sep 15 08:30:43 PDT 2012

On Sat, Sep 15, 2012 at 8:10 AM, Mikalai Lapkouski <gort105 at gmail.com> wrote:
> 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.  (This is basically what AutoBuild's omit map
feature does internally.)

> 2. Next, I wanted to generate a composit_sa_omit map as in this case DNA
> would be deleted in small portions and the resulted map would give me a map
> I can use for publication:
> phenix.autobuild data=inp.mtz model=whole.pdb (contains DNA) maps_only=True
> (to skip rebuilding) composite_omit_type=sa_omit omit_selection=DNA.pdb
> (contains only DNA coordinates). But the job runs too long and still it
> seems like it is doing rebuilding. Is this a correct command and correct
> action to create a sa_omit map for the DNA in my complex?

My understanding was that the composite omit map generation always
works on the entire structure, not a selection of atoms.


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