Hi Ian, thanks - this makes it clear(er) to me. The unit [e/A^3] suggested an accuracy to me that isn't really there, while rmsd felt more what it really is (maybe only due to habit and training).
Cheers,
Tim
On Mon, 2 May 2022 15:27:13 +0100
Ian Tickle <ianj...@gmail.com> wrote:
> 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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--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna
Phone: +43-1-4277-70202
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