On Tue, Jun 02, 2009 at 12:57:59PM -0400, Ed Pozharski wrote: > I've seen this before in some structures and have verified in those > cases that correction of the bulk solvent mask fixes the negative > density. > ... > It was quite convincing that it's indeed empty cavities large enough > to be filled with artifact bulk solvent.
We do that by default in BUSTER now for ~5 years - also with good experiences (all assuming the data isn't particularly weird at the low resolution end - as discussed by others). > In general, my experience was that although the negative density > disappears, effect on R/Rfree is negligible (less than 0.1%). They seem > to be cavities made exclusively out of hydrophobic sidechains (i.e. > carbon-only), but may set of observations is, of course, limited. We see very rarely an increase in R/Rfree - but this nearly always points back to very poor data and/or extremely partial models. In the vast majority it doesn't hurt at all and in a lot of cases it gives some significant drop in Rfree (0.5%) and/or reduction of Rfree-R gap. But the nicest thing is: it makes looking at those Fo-Fc maps so much easier - you don't get distracted by negative difference density caused by wrong bulks solvent modeling. Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
