 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 1]](rr5077fig1mag.jpg)
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Figure 1
Illustration of the deformable elastic network (DEN) method. (a) A starting model (orange, left) is refined against experimental data such as a density map depicted by the green mesh. For DEN refinement, harmonic distance restraints (black springs) are defined between randomly chosen atom pairs in the starting model. During the refinement the equilibrium distances, dij(t), of the restraints are allowed to change, as exemplified for one particular restraint in (b). The initial restraint potential (black dashed curve) is moved (red curve) in order to better fit to the electron-density map (green) (more generally, the target function Etarget; equation 2). The minimum of the DEN potential, dij(t), is attached to the reference distance, dij(0), by another harmonic potential, the strength of which is determined by the parameter γ. The choice of the parameter γ therefore reflects the relative influence of the reference model and the experimental data. |
![[Figure 1]](rr5077fig1.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
