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] mailto:[email protected] tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
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