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The main advantage of contouring in absolute units is consistency. The density for a water molecule with a B factor of 20 A^2 will look about the same even if the "noise" level of one map is higher than another. (Within limits, of course) This means that the actual value you contour at isn't as important as the choice of the same value all the time. You want to train your eye for what "good" density looks like at the level you use. I've picked 0.36 e/A^3 (don't get me started on units!) for density maps and 0.18 e/A^3 for difference maps as my personal values. The former is usually about 1 sigma and the latter about 3 sigma but of course the sigmas float based on other factors. I will look at the map contoured at lower levels when looking for atoms at lower than full occupancy, but I always start at the same place. When first learning model building it is useful to leave out a water molecule. That way you can see what a good water molecule looks like in your current difference map and can compare other potential water molecules to it. Dale Tronrud On 09/16/10 10:13, Nathaniel Clark wrote: > Hi, > It can, just do > fm-mode > select rmsd > > I am curious though, I have heard that it is 'better' to build in > units of absolute density, but I couldn't find any values. Does any > one have a suggestion as to what absolute electron density setting is > 'correct' for an Fo-Fc difference map? Or do you just eyeball it? > Nat > > On Thu, Sep 16, 2010 at 1:03 PM, Hailiang Zhang <[log in to unmask]> wrote: >> Hi, >> >> I generated a map using FFT, and tried to display it in O. By comparing >> with coot, I found that the "level" in O seems to be the absolute electron >> density instead of the sigma level. I am sorry I ask a question more >> related to O: can O draw the map by a given sigma level instead of the >> absolute density, just like coot? >> >> Thanks! >> >> Best Regards, Hailiang >>