Fig. 4.

(a) Distributions of corrections to interatomic distances calculated for structures obtained from MD simulations of the unit cell of ubiquitin's crystal, assuming three different types of motion: correlated (continuous blue curve), noncorrelated (broken red curve), and anticorrelated (dotted green curve). The distribution of differences between average interatomic distances and distances from average positions (also obtained directly from MD simulations) is shown as a continuous orange curve, with the arithmetic means and standard deviations for every distribution also given. All the values were binned in 0.04-Å bins to generate the distributions. Inset: Relationship between average instantaneous distances and corrections, assuming different types of motion. The percentage of atomic pairs whose average distance is closest to the one obtained from the corrections: 8.5% for correlated motion (blue), 90.2% for noncorrelated motion (red), and 1.3% for anticorrelated motion (green). (b) Normalized positional covariances between pairs of atoms used for calculations from an MD simulation of ubiquitin's crystallographic unit cell. Values are binned in 0.1 bins and color coded according to the closeness of the average distance to the correction for a specific type of motion (correlated, blue; noncorrelated, red; anticorrelated, green).