Wymol

Wymol is an interactive, browser-based protein interaction atlas and PDB structure viewer. It helps learners and researchers build intuition for the physical forces that stabilize protein structures and inspect atom-level interactions directly from PDB coordinates.

Wymol runs as a single HTML page. No installation or server is required for the built-in learning modules. English is shown by default, with Chinese available from the language switch.

Features

Interaction atlas

• Explains five underlying physical origins: electrostatics, dispersion/van der Waals forces, polarization, charge transfer, and solvent/entropy effects.

• Places common protein interactions on a logarithmic energy scale.

• Covers hydrogen bonds, salt bridges, cation–π and π–π interactions, CH–π and S–π contacts, disulfide bonds, metal coordination, hydrophobic contacts, halogen bonds, water bridges, and n→π* interactions.

• Shows the atoms or functional groups involved, common residues, approximate energy ranges, and geometry notes.

• Filters interactions by strength, biological system, and dominant physical origin.

Amino-acid explorer

• Browse all standard amino acids.

• Select a residue to see the interactions it can form and the structural roles it commonly plays.

• Open detailed explanations for each linked interaction type.

PDB interaction viewer

• Load a local .pdb, .ent, or text-format PDB file by clicking or dragging it into the page.

• Fetch a structure by entering a four-character PDB ID.

• Start quickly with the included example structures.

• Detect atom-level interactions from distance and angle rules directly in the browser.

• Visualize detected contacts on a 3D structure with lines or directional arrows.

• Select one or multiple residues, search by residue name or number, and inspect their interaction lists.

• Toggle residue labels and water molecules.

• Estimate interaction energies and report interaction occupancy for multi-model structures such as NMR ensembles.

• Display hydrophobic burial as a surface-based effect rather than a fictitious “hydrophobic bond.”

How to use Wymol

Open the application

Open pages/chemistry/Wymol.html in a modern desktop browser, or use the published version:

https://wangqian2149185.github.io/pages/chemistry/Wymol.html

The learning atlas works directly from the HTML file. Internet access is needed when fetching a PDB ID and when loading the 3Dmol.js viewer.

Explore the interaction reference

1. Read The five physical origins to understand the components behind named interactions.

2. Use the energy-scale chart to compare typical interaction magnitudes.

3. Filter the interaction cards by strength, system, or physical origin.

4. Click a card to open its detailed explanation, geometry, and energy information.

5. Select an amino acid in By amino acid to review the interactions available to that residue.

Analyze a protein structure

1. Scroll to Upload PDB · structural interaction viewer.

2. Choose one input method:

   • Drag a local PDB file into the upload area.

   • Click the upload area and select a file.

   • Enter a PDB ID and select Fetch.

   • Choose one of the example structures.

3. Wait for Wymol to parse the coordinates and detect interactions.

4. Click a residue in the 3D viewer or residue list.

5. Review its atom-level contacts, distances, directions, estimated energies, and occupancy values.

6. Hold Ctrl on Windows/Linux or ⌘ on macOS while clicking to select multiple residues.

7. Use Residue labels and Water to adjust the structural view.

Interpretation notes

• Reported energies are approximate interaction energies for teaching and exploration; they are not rigorous binding or folding free energies (ΔG).

• Geometry-based detection depends on the quality, protonation state, alternate conformations, missing atoms, and resolution of the input structure.

• Occupancy from a multi-model PDB describes how often a geometry is detected across the supplied models. It is not a molecular-dynamics probability unless the models come from an appropriate ensemble.

• Hydrophobic stabilization is a solvent-driven free-energy effect. Wymol separates it conceptually from direct dispersion and steric contacts.

• Quantitative conclusions should be validated with experimental evidence or appropriate molecular simulation and quantum-chemistry methods.

Privacy

Local files are parsed in the browser. Wymol does not upload local PDB files to an application server. Fetching a PDB ID sends a request to the public RCSB PDB file service, and the 3D viewer library is loaded from a public CDN.

Browser support

Use a current version of Chrome, Edge, Firefox, or Safari. A desktop browser is recommended for the 3D viewer and dense interaction panels.