[phenixbb] SA omit map

Pavel Afonine PAfonine at lbl.gov
Thu Sep 10 21:00:41 PDT 2009

Hi Pascal,

> I have a theoretical/practical question about omit maps and refinement.
> I am completing the refinement (in Phenix) of a protein-ligand complex 
> at 1.3A resolution. I solved it by MR and automatic rebuilding of the 
> protein alone first then built in the ligand. Rfree and Rfac are 
> 19.4%/18.2% after TLS and water-picking in Phenix. The model includes 
> everything protein, water, ligand and some ions.

Just a few remarks:

- At this resolution you should refine individual anisotropic ADPs, 
rather than constrained ADPs (using TLS model), for all macromolecular 
atoms. You may try to do so for water as well, but I would try both and 
see which gives more reasonable Rwork, Rfree and Rfree-Rwork;

- Riding H atoms should be included as well;

- As a final step, you may want to run the refinement with 
"optimize_wxc=true optimize_wxu=true" which may take a while to run, but 
will optimize relative X-ray/Restraints weights.

> However I have some slight doubts one region in my ligand.
> What would be the best map, less biased, to look at this "very late" 
> stage of the refinement. Are composite or systematic SA omit map 
> useful options at this stage ?

As a possible and easy to do option you can use Average Kick Maps, which 
we recently implemented in PHENIX. For details, here is the reference:
Acta Cryst. (2009). D65, 921-931. "Averaged kick maps: less noise, more 
signal...and probably less bias".

I just noticed Tom's reply, but since I went this far, I will continue 
and send my version of the reply as well...

In summary, the idea is:
An average kick map (AK map) is computed as following (Gunc(ar et al., 
2000; Turk, 2007; Pražnikar et al., 2009): a large ensemble of 
structures (several hundreds) is created where the coordinates of each 
structure from the ensemble are all randomly shaken. The shake amount 
(rmsd distortion introduced to coordinates) varies from 0 to 1.0 Å. Then 
for each structure a map is computed ((mFobs-DFmodel)exp(i?model) or 
(2mFobs-DFmodel)exp(i?model) or any other map, for example a ligand-omit 
map). Finally, all maps are averaged out to produce one averaged kick 
map. An AK map is expected to have less or no bias, less noise, enhance 
existing signal and potentially can clear up some initially bad densities.

So, to compute it, omit the ligand from your structure and follow the 
example in Tom's email.


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