On 19 May 2010, at 00:36, Paul Emsley wrote: > Jay Pan wrote: >> Hello Everyone, >> >> I have a reasonably well fitted electron density map through molecular >> replacement. However, there is always some red region left no matter how >> hard I tried when the mtz file is loaded into Coot. Is this because my model >> is still not good enough or it’s natural to most model fittings. In another >> word, should I be worried about the red region? Thanks in advance. > > Turn up the contour level and make it go away - that's what I do :) > > 3 or 3.5 sigma peaks are typical. Metals, carboxyls and disulfides are often > associated with relatively strong negative density, some people try adjust > their model to compensate (and others not, of course). As a rule of thumb, if > you have 5 sigma peaks at the end of your refinement, that might be > worrying/interesting.
The median height of the tallest positive peak after autoBUSTER re-refinement for the PDB *depositions* during April this year is about 7.2, and of the tallest negative peak about -5.0. 25/50/75th quantiles: negative peaks -5.9 / -5.0 / -5.6 positive peaks 6.1 / 7.2 / 8.6 Tom Womack (Global Phasing)
