Hi,
On Tue, Jul 14, 2026 at 02:04:02PM -0700, Dale Tronrud wrote:
> What people almost universally do is simply calculate the rms value of
> the map which is an rms deviation assuming the the "true value" is zero.
Out of interest: I understand the computation of "the" rms value for a
crystallographic map covering a multiple of the asymmetric unit -
which is standardising this computation to a large extent. But how
does one do this with EM maps? The map is in some kind of arbitrary
box and could be masked/non-masked ... so a rms value adequate for
visualising one map could be completely different for another map just
because of those technicalities, right?
I don't even pretend to understand the scale of those maps or any
other procedure that resulting in them, but is htere any standard
procedure that allows users to come up with a "typical" rms value that
would allow some kind of equal footling comparison between e..g
deposited EM maps? The rms level at which the lowest B TRP/PHE/TYR
shows a hole (just to pick "something" probably rather silly)?
Any pointer for my education about Cryo-EM SOPs would be highly
appreciated!
Cheers
Clemens
PS: we have the same problem in MX when dealing with deposited
non-crystallographic maps (like event maps in an abritrary P1 cell
with some padding around a masked density) ... as soon as we don't
have a defined standard volume (asymmetric unit) using the
resulting rms becomes an arbitrary choice in itself I guess.
> While you might be able to convince yourself that the rms value of a Fo-Fc
> map is related to its "error level" (although don't say that in the presence
> of James Holton!) no on can argue that the rms value of a density (or
> potential) map has any relation to the standard deviation of that map.
>
> So, Coot labels the quantity an rms. I, personally, hope that others
> would become honest about their calculation and use that term too.
>
> Dale Tronrud
>
> On 7/14/2026 6:45 AM, Morici, Martino wrote:
> > Hi folks
> >
> >
> > I am working on a CryoEM map of a ribosome (specifically a 70S .mrc from
> > Relion, looking at both the 3Drefined map focus-refined with a mask on
> > the 30S and the corresponding Relion postprocessed map with the same
> > mask).
> >
> > My aim is evaluating which parts of a ligand´s density appear at
> > lower/higher threshold.
> >
> >
> > In the field, the sigma is used (The ligand is visible at X sigma etc).
> >
> > Coot shows RMSD while scrolling.
> >
> > I did some homework and it seems to me that a certain value Y rmsd in
> > Coot is basically equivalent to the corresponding X sigma.
> >
> >
> > However, before publishing this and writing it down, I wanted your
> > opinion if effectively X and Y are the same, and if not how to
> > understand their correlation.
> >
> >
> > I am asking because I am not sure whether the way I processed these maps
> > may affect the X/Y correlation.
> >
> >
> > Thank you so much
> >
> > - M.
> >
> >
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*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., 9 Journey Campus, Castle Park
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