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Refinement: Difference between revisions
→Bulk solvent correction produces difference density: correction - "positive difference density " should in fact be "negative d.d."
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Sometimes people observe strong residual difference density in a cavity of the protein. E.g. there was a paper by Brian Matthews' group (Marcus D. Collins, Michael L. Quillin, Gerhard Hummer, Brian W. Matthews, Sol M. Gruner, Structural Rigidity of a Large Cavity-containing Protein Revealed by High-pressure Crystallography, Journal of Molecular Biology, Volume 367, Issue 3, 30 March 2007, Pages 752-763, [http://dx.doi.org/10.1016/j.jmb.2006.12.021]) on a high pressure form of lysozyme where they found a large hydrophobic void. Bulk water could only be compelled to enter the void by application of very high external pressure. | Sometimes people observe strong residual difference density in a cavity of the protein. E.g. there was a paper by Brian Matthews' group (Marcus D. Collins, Michael L. Quillin, Gerhard Hummer, Brian W. Matthews, Sol M. Gruner, Structural Rigidity of a Large Cavity-containing Protein Revealed by High-pressure Crystallography, Journal of Molecular Biology, Volume 367, Issue 3, 30 March 2007, Pages 752-763, [http://dx.doi.org/10.1016/j.jmb.2006.12.021]) on a high pressure form of lysozyme where they found a large hydrophobic void. Bulk water could only be compelled to enter the void by application of very high external pressure. | ||
Bulk solvent mask artifacts can only occur at narrow channels, where the mask radius is too big to define the channel as belonging to the bulk solvent region, leaving it "empty" and thus resulting in '' | Bulk solvent mask artifacts can only occur at narrow channels, where the mask radius is too big to define the channel as belonging to the bulk solvent region, leaving it "empty" and thus resulting in ''negative'' difference density. | ||
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. | ||