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

[Wei Shi]

 Hi all,
I am working with a protein dimer-ligand structure (resolution: 2.8Å) and
am going to make a figure showing the bound ligand superimposed with the
electron density (Fo-Fc) map obtained after omit refinement.
What I did is to make the ligand-free structure model and then use
Phenix.refine using the following parameters plus simulated annealing
(torsion angle) or (Cartesian):
Default: XYZ coordinates + Real-space+ Individual B factors + Occupancies.
Also click: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP
weight + Secondary structure restraints + NCS.

Contoured at 2σ, the Fo-Fc map generated show green density for most part
of the ligand, but for several atoms in the middle of the ligand, the green
density is missing... It's like this: some atoms have green density and the
next few no green density and then a couple few has green density and then
a couple more no green denisty.... The missing green density usually means
that part is disordered in the structure, right? I am not sure why the
density is missing for some atoms in the middle of the ligand. It would
makes more sense if the missing green density is at the end of the ligand...

Does anyone happen to have any clue about what it means for the green
density missing in my case?

Also, I am not sure whether I did the omit refinement right:
(1). For simulated annealing, it has two options, one is Cartesian and the
other is Torsion angle, and it's said that torsion angle is more suitable
of low resolution data. Is there any difference about which one to choose
in my case?
(2). Is it Okay to run the omit refinement in the presence of the following
parameters as I did:
Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight +
Secondary structure restraints + NCS.

Thank you so much!

Best,
Wei
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