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

Sam Stampfer Samuel.Stampfer at tufts.edu
Mon Dec 3 09:09:05 PST 2012

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

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!


PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3
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