[Chimera-users] map sigma

[Elaine Meng]

Hi Dieter,
Sigma generally means standard deviation, so we provide the rmslevel and sdlevel depending on whether the baseline is zero or the mean.

Normally contour levels are used to show all values greater than that level, so one would expect smaller volumes enclosed by contour levels at greater standard deviations. It doesn't really make sense to me the other way, otherwise the surface would enclose regions with essentially no data, zero density.

Maybe some of the EM experts and crystallographers on this list can say something about the official definition of sigma. The map expansion at greater sigma in the figure you referenced sounds backwards to me.  I didn't see much from "googling" but what I did found agrees with my intuition.
<https://www.quora.com/What-does-the-sigma-level-refer-to-in-electron-density-mapping>
<http://www.bioinformatics.org/molvis/edm/>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 5, 2020, at 10:44 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> 
> Dear Elaine,
> 
>     Thank you again! Unfortunately the meaning of 'sigma' in this context is still not clear to me [see e.g. Fig. 4 in  A. Bennett et al., Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2. J Struct Biol 209, 107433 (2020)]. In this figure they show a density map at sigma=1, sigma=2, and sigma=3, which is reflected in an the expansion of the map, i.e. in a DECREASE of the numerical value of the contour level. However, when I use these same values for sdLevel (i.e. vol #0 sdLevel 1, vol #0 sdLevel 2, and vol #0 sdLevel 3) I see the contrary i.e. the map is shrinking (i.e. an INCREASE of the contour level values of 0.00165, 0.0033, 0.00496, respectively). So, what do I misunderstand? How are 'sdLevel' and 'rmsLevel' correlated with 'sigma'?
> 
> bw Dieter
>