Here is what coot manual says about this,
> The density fit graph shows the density fit for residues. The score is > the average electron density level at the atom centres of the atoms in > the residue. The height of the blocks is inversely proportional to the > density average. > > The residue density fit is by default scaled to a map that is > calculated on the absolute scale. Sometimes you might be using a map > with density levels considerably different to this, which makes the > residue density fit graph less useful. To correct for this you can use > the scripting function: > > (set-residue-density-fit-scale-factor factor) > > where factor would be 1/(4\sigma_map) (as a rule of thumb). > > (residue-density-fit-scale-factor) returns the current scale factor > (default 1.0). > > On Fri, 2010-01-29 at 10:09 -0800, Ethan Merritt wrote: > I am wondering how the "goodness" scale for density fit analysis is > determined. > I have a case here where to the eye there is a very good fit of model to > density > throughout 99% of the unit cell, yet the validation tool marks most residues > with a big red bar. > > Is there some hidden property [e.g. map gradient?] that triggers a bad > validation score even though the fit to density looks fine by visual > inspection > at a single contour level? > > Is the good-to-bad scale normalized to the individual structure, so that > a 'good everywhere' structure looks 'uniformly bad' in the validation tool? > > Would the presence of large difference peaks outside the area of the current > model make any difference? > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
