Tunnel tutorial: cholesterol oxidase¶
This tutorial uses the bundled cholesterol oxidase structure, PDB 1MXT, to find routes from a known buried point and then compare them with a whole-structure origin search.
Objective¶
Run one explicit-origin tunnel search, inspect the candidate routes in VMD, and export the selected route with the inputs needed to repeat the analysis.
1. Load and select the structure¶
Load vmdhole/1MXT.pdb in VMD. Open VMDHole, select Tunnel, and set:
| Control | Value |
|---|---|
| Molecule | the loaded 1MXT molecule |
| Selection | protein |
| Frames | now |
The selection defines the molecular interior used by the search. Add a cofactor or bound ligand only when it should form part of that boundary.
2. Set and verify the origin¶
Leave Auto-detect origins off. Click the Start point field and paste
20.4632 0.4374 17.4692.
Open the MOLE parameters gear and enable Show cues. Confirm that the origin marker lies inside the protein. For another system, enter coordinates, use COG with a selection around the buried site, or use COR after centering the VMD view on the site.
3. Run the tunnel search¶
Keep the initial search parameters and select Run Tunnel. When the run finishes, the route table lists the accepted candidates. Select a row to display that route in VMD.
Inspect each candidate before using its measurements:
- the route begins near the requested origin;
- its centreline remains in accessible internal space;
- it reaches the molecular surface;
- its bottleneck lies on the displayed route rather than an unrelated groove.
If the routes start from the wrong cavity, correct Start point or the atom selection. If no route survives, inspect the origin first and then review the probe, interior, bottleneck, and minimum-length controls in the Tunnel workflow.
4. Inspect geometry and lining¶
Use the route table to compare rank, bottleneck radius, length, property summaries, and occurrence. Sorting the table changes its display order but not route identity.
Select Lining… for the current route and enable Show lining to display contacting residues and HET groups. Use the route gear to change its representation, material, or property coloring without rerunning the search.
5. Compare automatic origins¶
Enable Auto-detect origins (scan whole structure) and rerun. The explicit start point is disabled because it is not used in this mode. VMDHole now scans qualifying internal cavities and can return routes unrelated to the original site.
Treat this as a separate analysis question. Compare the starting regions and 3D paths, not only the route ranks. Disable automatic origins before returning to a site-specific search.
6. Export and record the analysis¶
Export the selected profile figure and CSV from the active plot tab. Use Lining… → Export to save lining data. Retain the saved run or manifest and record:
- structure, frame, and atom selection;
- explicit start point or automatic-origin setting;
- probe, interior, origin-radius, bottleneck, and length thresholds;
- weight function, exit constraints, and clustering settings;
- VMDHole and tunnel-engine versions.
For a trajectory, make the structure whole and image it consistently. Align trajectory is on by default in Tunnel mode; leave it on for cross-frame matching unless the trajectory is already aligned. It fits the loaded frames in VMD. Seen is the fraction of analysed frames assigned to the tracked route.
Citations¶
Before publishing, open Help → Guide & Citations… → Citations. Cite VMD, VMDHole, HOLE, and MOLE 2 for this workflow. Cluster within frame is on by default, so also cite CAVER 3.0 unless you disable clustering. See References for the full entries.
Continue with the Tunnel workflow.