Refinement: Difference between revisions

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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 ==
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