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Refinement: Difference between revisions
→Bulk solvent correction produces difference density
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The following advice is specific for [[ccp4dev:Refinement_with_Refmac5|Refmac]]: Changing from simple scaling to Babinet scaling is an important check to exclude mask bulk solvent artifacts, but there, you have to uncheck the "calculate contribution from the solvent region", because this is done by the Babinet scaling, already. | The following advice is specific for [[ccp4dev:Refinement_with_Refmac5|Refmac]]: Changing from simple scaling to Babinet scaling is an important check to exclude mask bulk solvent artifacts, but there, you have to uncheck the "calculate contribution from the solvent region", because this is done by the Babinet scaling, already. | ||
Alternatively, you can optimise the solvent mask parameters by running Refmac with the keyword "solvent optimise". This will write out R and R-free for different combinations of VDW probe, ion probe, and shrinkage sizes. For subsequent Refmac runs you can use the keywords "solvent vdwprobe $VDWPROBE ionprobe $IONPROBE rshrink $RSHRINK" replacing | |||
$VDWPROBE, $IONPROBE, and $RSHRINK with the optimal values from the previous optimisation or you can set these values in the GUI. | |||
If the peaks remain, try gradually reducing the size of the VDW probe. | |||
For [[Phenix|phenix.refine]], the bulk solvent mask may be varied - see [http://www.phenix-online.org/documentation/refinement.htm#anch52]. | For [[Phenix|phenix.refine]], the bulk solvent mask may be varied - see [http://www.phenix-online.org/documentation/refinement.htm#anch52]. | ||