I'm afraid I seriously mistrust the sigma and e/A^3 numbers reported
by Coot for ncs averaged maps. I work with a crystal with near perfect
6-fold ncs and the e/A^3 numbers make no sense. For a 2Fo-Fc style map
the e/A^3 values should be nearly the same after as before. They are not.
The sigma of an averaged map has a definitional problem - what is the
volume to normalized over. With a map with crystal symmetry the answer is
pretty clear, use the asymmetric unit. The asymmetric unit of an averaged
map will be the least-common-multiple of the rotated unit cells and could
easily measure in hundreds if not thousands of unit cells. Not very
practical and not very useful. Paul says that he normalizes over a box,
which is the easy way out, but I don't believe it has any statistical meaning.
The box will contain some parts of the ncs asymmetric unit multiple times,
and include some cs related regions.
My opinion is that the e/A^3 calculation for ncs averaged density in Coot
is broken. (I have not used the daily-build version, just the stable releases,
but none have worked in my hands for years.) I usually contour an unaveraged
map at my desired level, and then adjust the averaged map so that it mostly
matches those contours. If your ncs is less perfect this will not work as
well for you.
Dale Tronrud
On 6/6/2012 2:20 PM, Paul Emsley wrote:
On 06/06/12 21:47, Ursula Schulze-Gahmen wrote:
I calculated threefold averaged omit maps in coot. These maps look nice and
clean, but I am having trouble making sense of the displayed sigma levels or
e/A3 values. When I display the unaveraged and averaged maps at a similar
density level for the protein the unaveraged map is at 0.024 e/A3 and 2.7
sigma, while the averaged map is displayed at 0.0016e/A3 and 7.6 sigma. I read
the previous discussion about this issue where it was recommended to rely on
the e/A3 values for comparison, but even that doesn't seem to work in this case.
Don't forget that in one case you are looking at a whole map and in the other
(an average of) maps generated from a box encapsulating each chain. I wouldn't
stress if I were you...
Paul.
