Mole3 Vibe tunnel analysis

Interactive tunnel and pore exploration

Input

PDB ID Structure unit

Biological assembly is useful for oligomeric pores; asymmetric unit uses the deposited coordinates only.

Biological preset

Preset

Expert overrides

Leave fields empty to use the selected preset. Reset clears all overrides back to preset defaults.

Target / bottleneck radius Å Probe radius Å Interior threshold Å Bottleneck tolerance Å Min depth Min depth length Å Surface depth threshold Å Min buried fraction Min tunnel depth Å Min origin depth length Å Min origin depth Min tunnel length Å Min directness Min endpoint distance Å Membrane endpoint margin Å Min membrane penetration Min membrane opposition Max pore pairs / cavity Max exit depth Å Surface cover radius Å Max exits / cavity Origin cover radius Å Origin radius Å Max water origins Min ligand atoms Max profile radius Å Max mean radius Å Similarity cutoff Similarity distance Å Profile samples Max origins / cavity Max tunnels Origin residue Origin chain Weight

HETATM obstacles Water origins Exit semantics Pore search

Include hydrogens Include waters as obstacles Do not prune shallow layers Disable cofactor origins Disable ligand origins Disable deterministic jitter

Scene settings

Tunnel display Tunnel colour Mesh quality Tunnel opacity