Refinement: Difference between revisions

Refinement (edit)

700 bytes added , 27 May 2011

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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.
+== 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''.