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. 2006 Aug 4;91(11):4121–4132. doi: 10.1529/biophysj.106.082099

FIGURE 4.

FIGURE 4

Axes of curvature of the initial (A) and final (B) snapshots of the NCP-DNA (dark) and the Ideal-DNA (light) simulations. Both structures represent the winding of the DNA in the nucleosome, but the kinks are initially present only in the NCP-DNA; the Ideal-DNA is in an ideal, smooth superhelical conformation at the start of the simulation. No histone core is present in either case, but all-atom harmonic restraints (0.1 kcal/mol/Å2) are used to keep the structures close to their respective initial conformations.