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Refinement: Difference between revisions
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→Bulk solvent correction produces difference density
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The other possibility of course is that the data is good, that this is an accurate experimental result and there really is a void, or at least a cavity where the mean bulk density is lower than in bulk water. One way to test the void theory would be to fill the cavity with O atoms of zero (or very small, say 0.01) occupancy. Hopefully (!) that will prevent Refmac filling the cavity with bulk solvent. One could then try giving these O atoms large B factors, say 200, to smear them out, and then increase the occupancies to titrate the actual bulk density. | The other possibility of course is that the data is good, that this is an accurate experimental result and there really is a void, or at least a cavity where the mean bulk density is lower than in bulk water. One way to test the void theory would be to fill the cavity with O atoms of zero (or very small, say 0.01) occupancy. Hopefully (!) that will prevent Refmac filling the cavity with bulk solvent. One could then try giving these O atoms large B factors, say 200, to smear them out, and then increase the occupancies to titrate the actual bulk density. | ||
Since 2016, so-called [https://www.phenix-online.org/documentation/reference/polder.html Polder maps] in Phenix allow to calculate omit density without filling in water which may obscure a ligand. | |||
== Model correctly placed, but difference density remains after refinement == | == Model correctly placed, but difference density remains after refinement == | ||