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Refinement: Difference between revisions
→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. | ||
== Model correctly placed, but difference density remains after refinement == | |||
# Fourier truncation ripples: | |||
#* [http://www.ccp4.ac.uk/newsletters/newsletter42/content.html CCP4 Newsletter] "On the Fourier series truncation peaks at subatomic resolution" by Anne Bochow, Alexandre Urzhumtsev | |||
#* Pages 52-55 here: [http://www.phenix-online.org/presentations/latest/pavel_validation.pdf] | |||
#* Oliver Einsle, et al. Science, 1696 (2002) 297 | |||
#* Page 267 Figure 4 in Acta Cryst. (2004). D60, 260-274 | |||
# Try: | |||
#* refine individual anisotropic ADP for these atoms (and isotropic for the rest); | |||
#* refine occupancy; | |||
#* define charge in input PDB file; | |||
#* if it is anomalous scatterer use and refine f' and f''. | |||