[phenixbb] Fo-Fc omit map for ligand in the protein-ligand structure

Nathaniel Echols nechols at lbl.gov
Sun Sep 14 14:18:34 PDT 2014

On Sun, Sep 14, 2014 at 2:12 PM, Wei Shi <wei.shi118 at gmail.com> wrote:

> Thank you so much! I guess I will do as Pavel first suggested to define a
> box around the ligand and omit all the scattering inside the box (ligand
> and bulk-solvent) using CCTBX. I now got CCTBX installed on my computer and
> are trying to figure out ... Let me know if any of you happen to know how
> to define a box and omit all the scattering using CCTBX. Thank you so much!

I'm skeptical that this is worth investing a lot of time in.  Sophisticated
map calculations can be very useful for interpretation and building an
initial model, but you shouldn't need to resort to writing custom software
just to demonstrate that something is bound.  If I was a paper reviewer I
would ask to see the standard omit map, without any tricks.  (Actually, I'd
ask for the model and experimental data so I could calculate the map
myself, but I'm not sure how common this practice is.)

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