http://phenix.lbl.gov/pipermail/phenixbb/2009-August/013554.html Web(Anecdotally, we have found that phenix.refine often refines to much tighter RMSDs with similar R-frees to other programs. This may reflect different approaches used in the …
[phenixbb] Refinement of occupancy 0 residues - phenix.lbl.gov
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Should I refine occupancy of my ligand? ResearchGate
WebThis will improve the overall electron density map and the density for the ligand will be more clear. When you first model the ligand in the map, by default the occupancy will be 1.0. In the ... WebRegarding the error, I have noticed differences of 10% percent occupancy depending on what you set the starting occupancy before refinement. That is, if the starting occupancy starts at 1, you might end up with 50%, but if you start it at 0.01, you might get 40%. WebRefinement of occupancies only: % phenix.refine data.hkl model.pdb strategy=occupancies This will only refine occupancies for atoms in alternative conformations or for atoms having partial occupancies. If there is no such atoms in input PDB file, then no occupancies will … Phenix Documentation - Structure refinement in PHENIX The graphical interface for phenix.refine runs the unmodified command-line … For omit selections, None is equivalent to (not all); for rigid-body selections, … reddit nursing missed one assignment