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

Pavel Afonine pafonine at lbl.gov
Mon Dec 3 19:54:40 PST 2012

Hi Sam,

I have a guess that may explain this. Scaling in case of twining and no 
twinning is done by two different routines. If I recall correctly one 
divides map coefficients by overall scale (no twinning) and the other 
(twining) doesn't. Sigma-scaled maps are not sensitive to this but 
volume scaled maps would be different by the factor of that overall 
scale (that's what you observe I guess).

Fixing this is in my todo list (but it's not high up in priority as it's 
rather inconvenience than a real problem).

For now I would just use sigma-scaled maps and rely more on map shape 
when interpreting it.


On 12/3/12 9:09 AM, 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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