Hi Tim

I would say that it's not the displayed map density value in whatever units
that's arbitrary: it's completely defined as the true density on an
absolute scale minus the F000 contribution ('b' below) and optionally
divided by the RMS.  It's just that we don't have a good estimate of F000
and as I said it's your choice of contour level that's arbitrary.

The Buster map is scaled to the model so is on an absolute scale.  We can
write the linear transformation:

rho[map] = a.(rho[true] - b)

where the scale factor a = 1 so that rho[map] is on the same absolute scale
as rho[true] (i.e. differences in rho[true] are equal to differences in
rho[map]), and b is the F000 contribution.

Cheers

-- Ian


On Mon, 2 May 2022 at 15:04, Tim Gruene <tim.gru...@univie.ac.at> wrote:

> Hi Paul,
>
> I'd rather you comment on the unit "e/A^3" displayed at the top of my
> Coot canvas when I change the contour level of a map. Is this arbitrary?
>
> I noticed that the Buster Wiki states that their FWT is on an absolute
> scale. Would there be a paper or url to advance my rusty habits?
>
> Cheers,
> Tim
>
>
> On Mon, 2 May 2022 13:52:05 +0100 Paul Emsley
> <pems...@mrc-lmb.cam.ac.uk> wrote:
>
> > On 02/05/2022 12:44, John R Helliwell wrote:
> > > I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather than
> > > 3.
> >
> >
> > It's 5.6 now :-)
> >
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> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
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