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![[Figure 3]](qj5007fig3mag.jpg)
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Figure 3
(a) 15 residues in a polyalanine β-sheet with the β-loop showing average positions described by 45 backbone torsion angles. (b) The array of n individual conformers, from which the average in (a) was derived, is shown here with no additional flexibility (n = 120). (c) The array in (b) has been modified by using an applied equal forward and backwards kick (one parameter, target Cα marked with an arrow) propagated in both directions to introduce flexibility in the β-loop, producing a variable torsion angle in the two bonds linked to the Cα atom between elements of the array (n = 120). (d) The same model as in (c) but with increased sampling (n = 300). Increasing the sampling does not increase the number of parameters. (e) Workflow for the fitting procedure in Vagabond. (f) The effect of small perturbation of the Ramachandran bond torsion angle against the change in r.m.s.d. of each Cα atom-point cloud for PDB entry 5g5y chain A. Red denotes an increase, grey no change and blue a decrease. Lines denote visually separable domains. (g) Marked boundaries from (f) on the polypeptide chain, shown as orange → blue → yellow → magenta, drawn with PyMOL (DeLano, 2002  ). |
![[Figure 3]](qj5007fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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