Figure 9.

Spatial representation of reference (left) and recovered (right) conformation ensembles for bead chains of 45 beads with (a) four free loops and (b) four tied loops. Each depicted ensemble consists of 100 conformations extracted at equal intervals from 10⁸ steps of BD simulation and aligned on the beads that were connected by harmonic restraints in the simulations used to generate the reference ensembles. The coloring order along each chain is red, yellow, green, cyan and blue. Images were generated using UCSF Chimera (48).