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.

Pavel

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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