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 /
