Hi, I have a crystal structure at 3A resolution with six copies in the asu. When I average the map over the ncs I find that the original 2Fo-Fc style map has a sigma of 1.5 at 0.3 e/A^3. When I adjust the contour level of the averaged map to match, by eye, the level of the unaveraged map I find them equivalent at a sigma of 2.6 at 0.28 e/A^3. These results imply that the "sigma" level of the original map was 0.2 e/A^3 and the averaged map was 0.11 e/A^3.
The "sigma" of a 2Fo-Fc style map is not an estimate of uncertainty, of course, because nearly everything in the map is signal. It is just a measure of the variability of the signal, i.e. the rms. With averaging the signal should be preserved and the noise reduced, but the noise of a 2Fo-Fc map is small compared to the signal. How is it that the rms of my averaged map drops to half of the unaveraged value and yet the electron density looks about the same when contoured at the same e/A^3 (0.3 vrs 0.28)? I guess the real question is, how does Coot calculate the "sigma" of an averaged map? You can't calculate the rms over the asymmetric unit because the asymmetric unit is many millions of unit cells in size (and hugely variable depending on small changes in the ncs operators). The problem at hand is that I want to quote the sigma level I insisted upon when creating water molecules and think it will sound weird if I say I used a value of 12, which I did. The numbers just don't seem right to me so I'd like a little reassurance. Dale Tronrud
