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Refinement: Difference between revisions
→Bulk solvent correction produces difference density
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If the peaks remain, try gradually reducing the size of the VDW probe. | If the peaks remain, try gradually reducing the size of the VDW probe. | ||
For [[Phenix|phenix.refine]], the bulk solvent mask may be | For [[Phenix|phenix.refine]], the bulk solvent mask may be optimized using "phenix.refine data.hkl model.pdb optimize_mask=true" - see [http://www.phenix-online.org/documentation/refinement.htm]. | ||
In the case of ''negative'' difference density in a big hydrophobic cavity, one possible reason for a negative difference density are underestimated magnitudes of |Fobs| at very low resolution, either because they are weakened by the beam-stop (half-)shadow, or because they are overloads that have been poorly extrapolated. A simple check for wrongly determined low-resolution |Fobs| is to cut your low resolution data during refinement at a somewhat higher resolution, say 20 A instead of 80 A, and see whether the negative difference density disappears. If, yes, you should check your data processing again. | In the case of ''negative'' difference density in a big hydrophobic cavity, one possible reason for a negative difference density are underestimated magnitudes of |Fobs| at very low resolution, either because they are weakened by the beam-stop (half-)shadow, or because they are overloads that have been poorly extrapolated. A simple check for wrongly determined low-resolution |Fobs| is to cut your low resolution data during refinement at a somewhat higher resolution, say 20 A instead of 80 A, and see whether the negative difference density disappears. If, yes, you should check your data processing again. | ||