Molstar Lite
Lightweight yet powerful — a molecular structure toolkit for VS Code, powered by Mol*.
Browse, compare, and explore molecular structures directly in VS Code. Open a single file for detailed analysis with full Mol* controls, or open an entire folder to browse hundreds of structures in a grid view — folders open instantly, no matter how many files.
✨ Features
🗂️ Grid View
Open multiple files or a folder to view structures as a grid of interactive cards.
- 🖼️ Thumbnail preview — Lazy-rendered 3D thumbnails for each structure
- 🖱️ Click to activate — Click a card to preview with an interactive 3D overlay; double-click or press
Enter to open in full viewer
- 🎨 Toolbar controls — Change color scheme, representation, rendering style, and grid size across all cards
- 🔍 Search, sort & filter — Search by filename, sort by name, filter by format (with file counts)
- ✅ Selection mode — Select cards with click,
Ctrl+Click, or Shift+Click for range selection; delete with undo support (Ctrl+Z)
- ⌨️ Keyboard navigation — Arrow keys to navigate,
Enter for full viewer, Escape to go back
🔬 Full Viewer
Double-click any card to open the full Mol* viewer with complete controls — sequence panel, component management, representation editor, and more. Each card remembers its own viewer state independently.
🌈 Syntax Highlighting
Built-in semantic syntax highlighting for molecular file formats. Opens automatically when you edit any supported file — no extra extension needed.
- 🧬 Residue coloring — Amino acids colored by biochemical property (hydrophobic, polar, positive, negative, special)
- ⚛️ Element coloring — Atom symbols colored using CPK convention (C, N, O, S, H, P, metals)
- 🏷️ Structural records — ATOM/HETATM, HELIX, SHEET, SSBOND, chain IDs, coordinates, B-factors
- 🧪 Nucleotide coloring — DNA (A/T/G/C) and RNA (A/U/G/C) bases with distinct colors in FASTA files
- 🔧 GROMACS toolkit — MDP parameters, topology sections, preprocessor directives, index groups, XVG data
- ⚙️ Fully configurable — Customize all residue and element colors via
Settings > Molstar Lite
🚀 More
- 👆 One-click preview — Click the molecule icon in the editor title bar to instantly visualize a structure
- 📂 Open files or folders — Right-click in Explorer, use the Command Palette, or click the Open button in the viewer
- 🔄 Recursive folder scan — Right-click a folder and choose "Open Folder Recursively" to find all molecular files in subdirectories, with a confirmation dialog before opening
- 🌐 Works with VS Code Remote — Full support for SSH, WSL, and container environments
| Format |
Extension |
Description |
3D Viewer |
Syntax Highlighting |
| PDB |
.pdb |
Protein Data Bank |
✓ |
✓ |
| PDBQT |
.pdbqt |
AutoDock |
✓ |
✓ |
| PQR |
.pqr |
PDB with charge & radius |
✓ |
✓ |
| mmCIF |
.cif .mmcif |
Macromolecular CIF |
✓ |
✓ |
| GRO |
.gro |
GROMACS coordinate |
✓ |
✓ |
| MOL |
.mol |
MDL Molfile |
✓ |
✓ |
| MOL2 |
.mol2 |
Tripos Mol2 |
✓ |
✓ |
| SDF |
.sdf |
Structure-Data File |
✓ |
✓ |
| XYZ |
.xyz |
XYZ chemical file |
✓ |
✓ |
| FASTA |
.fasta .fa .fna .faa .ffn .fas |
Sequence file (protein & nucleotide) |
— |
✓ |
| MDP |
.mdp |
GROMACS parameters |
— |
✓ |
| TOP |
.top |
GROMACS topology |
— |
✓ |
| ITP |
.itp |
GROMACS include topology |
— |
✓ |
| NDX |
.ndx |
GROMACS index |
— |
✓ |
| XVG |
.xvg |
Grace/GROMACS data |
— |
✓ |
🏁 Getting Started
- Install from the VS Code Marketplace
- Open a molecular file and click the molecule icon in the editor title bar
- Or right-click a file/folder in the Explorer and select Molstar Lite: Open
- Or right-click a folder and select Molstar Lite: Open Folder Recursively to scan all subdirectories
- Or select multiple files in the Explorer, right-click and open them together in grid view
- Or press
Cmd+Shift+P / Ctrl+Shift+P and run Molstar Lite: Open
💻 Commands
| Command |
Context |
Description |
Molstar Lite: Open |
Single file |
Open one molecular file in full viewer |
Molstar Lite: Open |
Multiple files |
Select multiple files in Explorer → right-click → open all in grid view |
Molstar Lite: Open |
Folder |
Open all molecular files in a folder (one level) |
Molstar Lite: Open to the Side |
Single file |
Open in a side panel (via editor title bar icon or editor right-click menu) |
Molstar Lite: Open Folder Recursively |
Folder |
Recursively scan all subdirectories and open all molecular files found |
Commands are available via the Command Palette, Explorer right-click menu, editor right-click menu, and the editor title bar icon.
⚙️ Settings
| Setting |
Default |
Description |
molstarLite.highlight.enabled |
true |
Enable/disable syntax highlighting |
molstarLite.highlight.residueColors |
(see below) |
Colors for amino acid groups |
molstarLite.highlight.elementColors |
(see below) |
CPK colors for elements |
Residue color groups: hydrophobic, polar, positive, negative, special, water, dna, rna, ligand
Element color groups: carbon, nitrogen, oxygen, sulfur, hydrogen, phosphorus, metal, other
⌨️ Keyboard Shortcuts (in viewer)
| Key |
Action |
Arrow keys |
Navigate between cards |
Enter |
Open active card in full viewer |
Escape |
Close full viewer / exit select mode / deactivate card |
Ctrl+A |
Select all cards (in select mode) |
Ctrl+Z |
Undo last delete |
Ctrl+Click |
Toggle card selection |
Shift+Click |
Range selection |
💬 Feedback
Found a bug? Have a feature request? Feel free to open an issue on GitHub.
🙏 Acknowledgments
Powered by Mol* — an open-source toolkit for molecular visualization (MIT License).
📄 License
MIT
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