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).

Thanks,
Pavel

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: [email protected]

tel (office): +44 (0)1273 678349

tel (lab): +44 (0)1273 677512
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