VMDHole documentation¶
VMDHole turns a structure or trajectory loaded in VMD into pore and tunnel profiles, linked 3D geometry, property annotations, trajectory-wide views, and exportable figures and tables. Independent frames run in parallel, and native engines accelerate production calculations.
Choose the analysis¶
| If you need to… | Use | Define first | Main results |
|---|---|---|---|
| Characterize one known channel through a structure or trajectory | Pore (HOLE) | A point inside the pore (CPOINT) and its direction (CVECT) |
Radius and cross-section profiles, Connolly lateral openings, Capsule geometry, conductance estimates, hydration, ion movement, and permeation |
| Find routes from a buried site to the molecular surface | Tunnel (MOLE 2) | A point inside the buried site, or automatic origins | Ranked and clustered routes, bottlenecks, lining residues, property annotations, and route occurrence across frames |
Both workflows keep plots, CSV data, and 3D representations connected to the current VMD frame. For method derivations and scientific validation, read the paper and cited methods; these pages focus on operating the plugin and reporting an analysis.
Start here¶
- Install VMDHole and native engines.
- Complete the first pore and tunnel analyses (highly recommended).
- Choose a tutorial for the analysis you need.
- Continue with the matching workflow.
- Consult the parameter reference for every control and default.
Analyse and interpret¶
| Page | Scope |
|---|---|
| Pore workflow | Define the channel, run HOLE, and use the pore analysis views |
| Tunnel workflow | Find, rank, cluster, track, and display routes |
| Parameter reference | GUI controls, defaults, radius files, and reporting values |
| Visualization | 3D representations, color, material, lining, and playback |
| Properties | Property definitions, averaging, and picker relationships |
| Exports | Figures, CSV tables, saved runs, and tunnel lining data |
| Files and settings | Output layout, persistence, caching, and performance controls |
| Scripting | Tcl and headless operation |
Verify and troubleshoot¶
| Page | Scope |
|---|---|
| Troubleshooting | Symptom-based diagnosis |
| Testing | The test tiers, every group and unit test, and the conventions they enforce |
| References | Methods, property scales, and required citations |
Before interpreting a result¶
Confirm all of the following:
- The atom selection contains the intended protein, cofactors, and blockers, but excludes irrelevant solvent or membrane atoms.
- The radius file covers every selected atom.
- The centreline or tunnel lies in the expected cavity in the 3D view.
- Periodic trajectories are made whole and consistently imaged.
- Frames are aligned when a fixed pore axis or cross-frame tunnel identity is used.
- The same method, radii, sampling, seed policy, and trajectory preparation are reported for comparisons.