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<div>Dear all,</div>
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<div>Apologies if this has been covered already in a previous post — but I can't find a suitable response in the archive.</div>
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<div>We have the following situation...</div>
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<div>We have soaked a ligand into an apo-crystal, collected diffraction data, and solved the structure.</div>
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<div>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%. </div>
<div>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.</div>
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<div>What I want to do, and can't quite get phenix.refine to do is the following...</div>
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<div>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.</div>
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<div>Could anyone help me with how the occupancies / constrained_group parameters should be set up in this case?</div>
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<div>With thanks,</div>
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<div>Tony.</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Dr Antony W Oliver
<div>Senior Research Fellow</div>
<div>CR-UK DNA Repair Enzymes Group</div>
<div>Genome Damage and Stability Centre</div>
<div>Science Park Road</div>
<div>University of Sussex</div>
<div>Falmer, Brighton, BN1 9RQ</div>
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<div>email: <a href="mailto:antony.oliver@sussex.ac.uk">antony.oliver@sussex.ac.uk</a></div>
<div>tel (office): +44 (0)1273 678349</div>
<div>tel (lab): +44 (0)1273 677512</div>
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