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!

Best,
Wei

On Sun, Sep 14, 2014 at 5:18 PM, Nathaniel Echols <nechols@lbl.gov> wrote:
On Sun, Sep 14, 2014 at 2:12 PM, Wei Shi <wei.shi118@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