[phenixbb] Sa_Omit_map_DNA_low_resolution

Nathaniel Echols nechols at lbl.gov
Sat Sep 15 13:38:30 PDT 2012

On Sat, Sep 15, 2012 at 1:19 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> Yes, that's the trick. We should streamline it somehow.

It's not clear to me why that parameter is True - in what other
circumstances would we expect to find zero-occupancy atoms?

A related question: what happens in phenix.maps when omit.selection is
set?  Right now, it looks like this simply deletes the selected
scatterers from the xray structure object, which I assume means the
bulk solvent mask will expand to fill the gap.  Wouldn't a better
method be to set the occupancies to zero and not ignore them when
calculating the mask?

> 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.

It's only about 1/8th of the structure (although those phosphates will
contribute a lot), so it shouldn't be too awful.  But at this
resolution I'm not sure what to expect.


More information about the phenixbb mailing list