Hi,
This is probably my fault since I convinced Paul to label this
quantity "RMSD". "Sigma" is generally interpreted to refer to the
"standard deviation" of the quantity, here electrostatic potential, and
a standard deviation is a measure of the "error" level which requires a
serious analysis and a clear definition of what you mean by "error".
This very difficult.
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. 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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