pyHole: An interactive tool for analysis and visualization of pores in macromolecules.

Authors

Briar Bell, Harikanth Venkannagari, Matthew L Baker

Published in

Biophysical journal. Oct 27, 2026. Epub Oct 27, 2026.

Abstract

Ion conducting pores and transport tunnels are often summarized by their centerline geometry, radius profile, bottlenecks, and lining residues, yet the tools most commonly used for such analyses are either dated, difficult to use, or unavailable locally on modern operating systems. Here we introduce pyHole, a lightweight, fully Python-based, cross-platform toolkit for rapid linear pore profiling and visualization from atomic structures. Given residue-defined bounds, pyHole traces a straight or curvature-aware centerline, evaluates the pore radius slice by slice, and reports accessible radii, lining residues, per-slice hydropathy or electrostatic indices, accessible and geometric volumes, and a simple geometric openness index. Results are written as portable CSV tables and as PDB representations (a centerline and a mesh surface) that render natively in molecular graphics software. A bundled ChimeraX extension provides an interactive front end so that users can select models and residue bounds in the viewer and immediately visualize the outputs. Altogether, pyHole provides a pragmatic and easy-to-use solution for characterizing channels within macromolecules.

PMID:
42935098
Bibliographic data and abstract were imported from PubMed on 27 Oct 2026.

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