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

Pavel Afonine pafonine at lbl.gov
Sat Sep 13 20:21:18 PDT 2014

Hi Wei,

> Yes, I think it's true that "if ligand density is strong enough it may 
> not be masked by the bulk-solvent completely".

indeed. You can verify it yourself by taking a few examples of 
protein-ligand complexes with ligand occupancy (or mobility or both) 
varying in some range.

> Hi Nat, you mentioned that
> 1. "I thought phenix.refine ignores zero-occupancy atoms when 
> calculating the bulk solvent mask?  In fact there is an option 
> specifically to toggle this option, and I've noticed very different 
> results with and without it."

Yes, results are expected to be very different for reasons I explained 
in previous email.

> 2. "Restraining the zero-occupancy ligand (and perhaps adjacent 
> residues) is strongly recommended, especially if it contains heavier 
> elements.  (The newer versions of the phenix.refine GUI have a button 
> in the Output tab to set this up.)  Without restraints, you run the 
> risk of refining the surrounding model into the ligand density.  As 
> always this is worse at lower resolution - at 2.8Å I'm not sure what 
> to expect."
> I am wondering how this could be done.

I am not sure why you may want to do this at all. If you keep the ligand 
in PDB file and "omit" it by setting occupancies to zero then the omit 
map you will get is useless if you ask the program to not fill bulk 
solvent into ligand region. If you let the program to fill bulk-solvent 
into ligand region (= ask mask calculation to ignore zero occupancy 
atoms) then why don't you just remove the ligand from PDB file (then you 
don't need to worry about restraining it etc.)? In fact you can even 
keep it in file as you don't care (for map calculation purpose) where 
restraints will move it.


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