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. 2008 Apr 18;95(3):1007–1017. doi: 10.1529/biophysj.107.122853

FIGURE 2.

FIGURE 2

Knock-out filter RMSD plots. (Top) The RMSD (Å) introduced by the knock-out filter is plotted versus the wavenumber, k, removed from all of the helical parameters simultaneously. The arrow indicates the location of k = 14, which corresponds to a length scale of 145/k = 10.36 bps. Structures are identified by their Protein Data Bank id code as indicated in the legend. 1kx3S represents an average structure obtained from a 10-ns molecular dynamics simulation of pdb entry 1kx3 (20). The horizontal line at 3.0 Å indicates our criteria for high resolution. The RMSD does not converge to 0.0 Å because we have set the intra-basepair helical parameter values to zero. (Bottom) The RMSD (Å) introduced by individual helical parameter knock-outs. Axes have the same scale as in the top graph. In these knock-outs, only the indicated helical parameter is subjected to filtering; the other parameters are obtained from the initial structure.