[phenixbb] Ligand / Loop occupancy refinement

Pavel Afonine pafonine at lbl.gov
Mon Sep 19 08:10:45 PDT 2011

Hi Tony,

could you please send me the PDB file or its part that contains all 
residues (atoms) in question, tell occupancies of which atoms should be 
refined and how, and I will send you back working example as soon as I can.

What you are trying to do is definitely possible to do in phenix.refine.

Please send files off list (to may email directly).


On 9/19/11 8:02 AM, Antony Oliver wrote:
> Dear all,
> Apologies if this has been covered already in a previous post — but I 
> can't find a suitable response in the archive.
> We have the following situation...
> We have soaked a ligand into an apo-crystal, collected diffraction 
> data, and solved the structure.
> What is apparent from the electron density,  is that the ligand isn't 
> in the crystal at full occupancy, it's roughly about 70-80%.
> However, as the ligand binds, it causes a small conformation change in 
> the active site of the protein, altering the position of around 4 
> amino acids.
> What I want to do, and can't quite get phenix.refine to do is the 
> following...
> Refine the occupancy of the ligand (chain C resname LIG) with the "A" 
> conformation of the active site residues (which should be the same, as 
> they are mutually dependent) — and then refine the occupancy of the 
> "B" conformation of the active site residues —  which should all 
> theoretically add up to a total of 1.
> Could anyone help me with how the occupancies / constrained_group 
> parameters should be set up in this case?
> With thanks,
> Tony.
> ---
> Dr Antony W Oliver
> Senior Research Fellow
> CR-UK DNA Repair Enzymes Group
> Genome Damage and Stability Centre
> Science Park Road
> University of Sussex
> Falmer, Brighton, BN1 9RQ
> email: antony.oliver at sussex.ac.uk <mailto:antony.oliver at sussex.ac.uk>
> tel (office): +44 (0)1273 678349
> tel (lab): +44 (0)1273 677512
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