[phenixbb] occupancy refinement

Pavel Afonine PAfonine at lbl.gov
Tue Nov 24 12:23:09 PST 2009

Hi Maia,

I presume you are refining one occupancy per whole ligand (asuming that the ligand site is partially occupied), and not individual occupancies one per atom.
I think the best criteria are:

- the refined values of overall occupancy and individual B-factors;
- electron density maps: 2mFo-DFc and mFo-DFc.

Depending on ligand size, or better say, on the ratio whole_model_size/ligand_size, the R-factors (Rfree, specifically) may not be the best measures since they may not be sensitive enough to very local changes. 


----- Original Message -----
From: chern at ualberta.ca
Date: Tuesday, November 24, 2009 12:08 pm
Subject: Re: [phenixbb] occupancy refinement
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> Hi,
> I am wondering what is the criteria for occupancy refinement of  
> ligands. I noticed that R factors change very little, but the 
> ligand  
> B-factors change significantly . On the other hand, the occupancy 
> is  
> refined to the second digit after the decimal point. How can I 
> find  
> out the error for the refined occupancy of ligands?
> Maia
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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