Refinement: Difference between revisions

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.
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''.
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