Biomolecule Viewer

A local-first molecular structure viewer for VS Code and code-server, powered by Mol*.

Open a structure

• Right-click a supported structure file in the Explorer and select Open with Biomolecule Viewer.
• Alternatively, run Biomolecule Viewer: Open Structure... from the Command Palette.
• To choose the viewer through VS Code's standard menu, select Open With... → Biomolecule Viewer.
• Drag structure files directly into an open viewer to load additional structures.

The extension uses a read-only custom editor with optional priority, so PDB and mmCIF files can still be opened as text normally.

Supported formats

PDB (.pdb, .ent, .pdbqt), mmCIF (.cif, .mmcif, .mcif, .bcif), GRO (.gro), XYZ (.xyz), MOL (.mol), MOL2 (.mol2), and SDF (.sdf, .sd). Extension matching is case-insensitive. Gzip files are not supported in this milestone.

Mol* provides sequence, selection, component, representation, measurement, visibility, and camera controls. All viewer assets are packaged locally; no CDN is required.

Build and install

npm ci
npm run check-types
npm run package
npx @vscode/vsce package --out biomolecule-viewer-0.1.0.vsix
code-server --install-extension biomolecule-viewer-0.1.0.vsix --force

Run Developer: Reload Window after installing or upgrading.

Current scope

This release establishes secure local loading, right-click opening, and drag-and-drop. PyMOL-style named selections and commands, explicit XTC/DCD trajectory pairing, and session restoration are planned subsequent milestones.

Acknowledgments

Built with Mol*. Inspired by VSCoding-Sequence / Protein Viewer. If Mol* is useful in research, cite Sehnal et al., Nucleic Acids Research 2021, doi:10.1093/nar/gkab314.