[ccp4bb] sigma levels of averaged maps in coot ( or e/A3)
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. Any suggestions? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
Re: [ccp4bb] sigma levels of averaged maps in coot ( or e/A3)
Ursula, please don't forget that you are looking at Fourier image of electron density distribution, which may be as different from the true electron density distribution as different from zero the F000 reflection and as different your Fobs data set from being 100% complete for all possible reflections. So all in all my suggestion is to not make too much sense of absolute values of the Fourier map you are looking at. Best, Pavel Afonine On Wed, Jun 6, 2012 at 12:47 PM, Ursula Schulze-Gahmen uschulze-gah...@lbl.gov 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. Any suggestions? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
Re: [ccp4bb] sigma levels of averaged maps in coot ( or e/A3)
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.
Re: [ccp4bb] sigma levels of averaged maps in coot ( or e/A3)
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.
