Fig 3. Comparison with a linearly interpolated path. A hypothetical transition pathway P (cyan line) in a 3D configuration space composed of a discrete number of conformer snapshots (cyan circles) connects an initial state (green circle), c0, and final state (red diamond), cf.
The reference path R (black line) is represented by LinInt. Each snapshot pk is associated with its projection, rk, on R; the progress, ζ(k), is the rmsd between rk and cf (dashed purple line along R) and the displacement, ρ(k), is the rmsd between pk and rk (dashed purple line perpendicular to R).