Later in refinement the missing water molecule will also have a higher
peak because the phases will be better (e.g. your R-free is 20% lower).
The fact that it was placed later in refinement both reflects the RMSD
effect but also reflects the fact that it's more obviously a legitimate
water
If you view the value of the density as the number of electrons per
cubic Angstrom relative to the local average it is both accurate and
precise. This framing avoids the most serious problems with a measure
based on the rms, such as the problem that the "rms" depends on the
particular
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 wrote:
> Hi Tim
>
> I would say that
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
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,
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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Dear Tim,
I recall initiating a similar thread, and question, some years back.
Ian may have answered similarly before.
I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather than 3. But in
practice as i delved in peaks below 5sigma I generally found, and still find,
in many cases what
Hi Tim
The absolute peak height doesn't only depend on the element, it also
depends on a number of other things, most notably the resolution and the B
factor (i.e. peaks are broader and peak heights are lower at lower
resolution and higher B factor), and of course the occupancy factor in the
case
Hi Ian,
this is the custom I was educated with. However, small molecule people
seem confused when a map contour level is described with an rsmd (which
to me makes some sense). When refining a structure with shelxl, the
peak height of the maxima of the difference map corresponds quite well
to the
Hi Tim
F000 is customarily not included in MX electron density for the reason you
mention. This doesn't matter because the contour levels are completely
arbitrary anyway, i.e. you choose a level that shows the features you
expect to see. This can be misleading of course since there may be
Hello readers,
how does Coot calculate the absolute map levels, i.e. the contour level
given as [e/A^3]? i always thought (rather from hear-say) that F000 was
necessary for the absolute level. With a small molecule structure, F000
can be calculated from a complete model, but with solvent
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