A map file stores a density value for each point on a grid. The units and nature of that item is not defined in the format of the map. A map can store any number of things. The actual values are defined by the process that created the map file.
For electron density maps you will find that some contain values measured in e/A^3, others contain values that are normalized Z scores (The standard deviation of the variation about the mean is set to 1.0), or just a bunch of numbers with arbitrary and mysterious units. One tends to use e/A^3 when trying to relate the map to expected electron density or to compare one map to another. A normalized map is useful if you are interested in the frequency that a density value of that magnitude appears in the map. (Is this value common or rare?) One uses arbitrary values if one has an attachment to honesty. Calculating an electron density map in units of e/A^3 is not an easy task. The diffracted intensities are not measured, themselves, in "real" units. Their magnitude only has meaning as intensities relative to the other intensities in the same dataset. For the map to be expressed in units of e/A^3 the diffraction intensities must be expressed in units of e/Unit Cell (at least that is the convention). This is a hard problem and many papers have been written on the topic. If you have a well refined and complete model for the contents of the crystal you can use the calculated diffraction pattern as a template to scale the observed intensities and calculate maps in e/A^3, but this is an approximation as no model is complete or completely correct. The other big issue is that we cannot measure the one reflection that defines the average of the electron density in the crystal. It happens to always hit the beamstop. Because of this problem our maps usually have an average value of zero, which is of course wrong. Even when the density values are expressed in e/A^3 the intention is that each value in the map must have a number added to it to achieve the true value at that point. At least it's the same number everywhere in the map, although we don't know its value. Because of these issues and uncertainties, when maps are compared they are usually compared using a correlation coefficient. The correlation coefficient is relatively unaffected by these scaling problems and will usually give the same answer when given any of the kinds of maps I described. If you want a more detailed comparison of electron density values you really have to get into the details of each of the datasets and scaling that was applied to ensure that your results are meaningful. Estimating the error bars of an electron density map is another enormous problem. As you would expect, it depends critically on the origin of the map. The error analysis of a map calculated from MAD phasing is quite different than that of a map calculated using a refined model as a reference. One complication is that the error level is not necessarily the same everywhere in the map. In addition the errors at different regions of the map are not independent. The correlation of deviations at different regions of the map are likely more important to any analysis then any simple overall error bar. However, if you insist on an error level, my best guess would be to identify the regions of bulk solvent and calculate the rms deviation from the mean there. Since these regions should be flat, and deviations from the mean must be due to something that does not represent election density. We might as well call it "error". Dale Tronrud Peter Schmidtke wrote: > Dear CCP4BB List Members, > > first of all I am not a crystallographer, but I would like to get some > things clear, things I did not find in "Crystallography Made Crystal Clear" > and on the internet for now. > > I am trying to read electron density maps in the EZD format. These maps > contain scaled values of electron density and size and shape of the unit > cell. How can I convert the values of intensities (what is the unit of > these values?) to the probabilities you can see in coot for example (1.03 > electron / A^3), > Once I have achieved this conversion, can I compare densities of different > maps of different proteins? If not directly, is there a way to do so? > > Last, is there a way to know the experimental error made on intensity > values of a map? > > Thanks in advance. > >
