Figure 4.

Timeline local cross correlation analysis (adapted from [92]). The Timeline plugin in VMD provides analysis and visualization of local structural properties such as cross correlation [92]. The structure in (a) is in the process of being fitted to the corresponding map in an MDFF simulation and is colored by the per-secondary-structure-component local cross correlation analysis (red is worst correlation, green is intermediate and blue is best). In this analysis scheme, the structure is split into contiguous sections of secondary structure which are used to calculate local cross correlations for each section independently. The Timeline window (b) shows the corresponding plot of local cross correlation of individual residues (y-axis) over time (x-axis) during the simulation. For example, two regions of relatively low correlation (colored red and green) have been highlighted in (a) and matched to the corresponding parts on the Timeline plot in (b). Both regions exhibit low cross correlation due to their varying degrees of distance outside of the density, but are fit as the MDFF simulation progresses, as evidenced in the Timeline plot.