Fig. 5.

Pore geometry calculations in CHAP. (A) Schematic representation of probe-based pathway finding. The position of a spherical probe is optimized in subsequent parallel planes to maximize its radius without overlapping the van der Waals sphere of any ion channel atom. (B) Configuration space view of probe positions (green spheres) in the permeation pathway of a 5-HT₃ receptor structure (PDB ID: 4PIR). For visual clarity, a large probe step of v = 1 nm was used here. (C) The probe center positions (blue spheres) are interpolated with cubic B-splines to yield a continuous spatial curve (green tube) representing the pore center line. (D) A surface representation of the channel pore is generated by extruding a circular cross section along the center line spline curve. (E) Convergence of the Nelder–Mead algorithm carried out to optimize the probe position in each parallel plane. The radius error falls below a threshold of 0.001 nm within 100 optimization steps irrespective of the value of the probe step. The reference radius profile is calculated with a very large number of 2000 Nelder–Mead iterations. (F) Influence of probe step on radius profile resolution. While a probe step of 0.5 nm only captures the general feature of the radius profile, decreasing the probe step from 0.1 to 0.05 nm leads only to minimal changes.