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

Wei Shi wei.shi118 at gmail.com
Sun Sep 14 14:31:22 PDT 2014

Hi Nat,
For standard omit map, do you mean using Phenix-> Maps -> Composite omit
map. And omit map method: Anneal and map types: 2mFo-DFc. Thank you so much!


On Sun, Sep 14, 2014 at 5:18 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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.)
> -Nat
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