Density Histogram

The density histogram is a discrete function that shows the number of voxels falling into a density value range, dt < d < di+1, as a function of the density d,-(see figure 6.9). Molecular boundaries are characterized as regions where the density falls from the protein or RNA value to the value of water. Voxels with densities intermediate between the two values are relatively rare. In the density histogram, we therefore expect to find two peaks, one for water, the other for protein/RNA, separated by a minimum. For density maps with sufficiently high resolution, the minimum may be easily determined, and can be used for

CFT-corrected 3D reconstruction

CFT-corrected 3D reconstruction

Figure 6.9 Density histogram of a 25-A reconstruction of the ribosome from cryo-EM data. Dashed line shows the histogram before CTF correction; solid line, after correction. The densities marked as d1 and d2 represent the volumes 3.4 x 106 and 2.4 x 106A3, respectively. From Zhu et al. (1997), reproduced with permission of Elsevier.

Figure 6.9 Density histogram of a 25-A reconstruction of the ribosome from cryo-EM data. Dashed line shows the histogram before CTF correction; solid line, after correction. The densities marked as d1 and d2 represent the volumes 3.4 x 106 and 2.4 x 106A3, respectively. From Zhu et al. (1997), reproduced with permission of Elsevier.

an objective determination of the density threshold representing the molecular boundary. Lower resolution maps present a problem since the ranking of densities is scrambled. For example, RNA bordering ice exhibits densities that range all the way from one extreme to the other, since sharp boundaries are "washed out'' into a margin of a width corresponding to the resolution distance. The histogram of such maps may, therefore, not contain clues about the placement of the threshold.

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