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Phenix: Difference between revisions
→An experimental feature currently being worked on
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=== Using dummy atoms to avoid bulk solvent to be filled in === | |||
Fill the space where the ligand is supposed to be with dummy atoms (DA), e.g. water, that all have zero occupancy. And when you run phenix.refine with those dummy atoms make sure you use "refinement.mask.ignore_zero_occupancy_atoms=False" keyword. Also, make sure you exclude the DA from coordinate (refine.sites.individual="not xxx") and ADP refinement (either refine.adp.individual="not xxx" or refine.adp.individual.isotropic="not xxx"), too. | |||
You can use [[Phenix#phenix.grow_density_-_local_density_improvement|phenix.grow_density]] to generate dummy atoms in spheres of defined radius placed in defined points. | |||
=== An experimental feature currently being worked on === | === An experimental feature currently being worked on === | ||