[phenixbb] Similar 2Fo-Fc maps, very different e/A^3 levels (absolute levels)

[Edward A. Berry]

I find that 1 "sigma" is about .3 absolute level in coot or O.
For order of magnitude reasonableness check,
   water is 55.5M x8 e- gives 444 mol/L
   which works out to .266 e-/A^3 average density
so if average gets set to zero, the minimum (between atoms where
there is nothing) would be about -.27, and the maximum something
like +.27 or greater (for atomic resolution maps).
So contouring at .004 or even .08 should be pretty similar to contouring at zero.
I suspect the maps are not on an absolute scale.


Sam Stampfer wrote:
> Dear Phenix group,
>
> I am trying to decide which electron density map to use for rebuilding my structure in Coot. Both 2Fo-Fc maps appear
> quite similar at the 1 sigma level but the absolute electrons per cubic Angstrom (e/A^3) is very different.
>
> When contoured at 1.00 rmsd in coot, these are the e/A^3 levels (Coot calls them absolute levels):
>
> Map #1 2Fo-Fc: 0.0044 e/A^3
>
> Map #2 2Fo-Fc: 0.0832 e/A^3
>
> Map #1 was generated using a twinning operator that is typically required for this crystal form. Map #2 was generated
> without the twinning operator and it tends to have slightly better 2Fo-Fc density, and there is a bit more density (or
> noise?) in the Fo-Fc map.
>
> The structure was refined in Phenix and gave a similar Rfree regardless of whether a twinning operator was used.
>
> What does it mean to have this 20-fold difference in electrons per cubic Angstroms for my maps? Which map should I use?
>
> Thanks for your help!
>
> -Sam
>
>
> PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3 level.
>
>
>
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