Rainbow mmCIF (VS Code Extension)
Enhanced syntax highlighting and visual aids for mmCIF (Macromolecular Crystallographic Information File) files, widely used in structural biology.
Designed to make reading and editing complex mmCIF files effortless. Unlike standard syntax highlighters, this extension focuses on human-readable visualization of data blocks, inspired by Rainbow CSV.
Features
Rainbow Block Highlighting
All data items — whether in a loop_ or a single-item section — are treated as a unified Block.
- Category (e.g.,
_atom_site) and Item (e.g., .id) are clearly distinguished with different colors
- Columns are automatically colored using a cycling rainbow palette to help you quickly align keys with their values
Integrated Dictionary Hover
Instant access to the official PDBx/mmCIF dictionary. Hover over any Category, Item, or data value to see its definition.
- Context-Aware: Dynamically displays documentation based on whether you hover over a Category, Item, or Value
- Direct Links: Quick navigation to official wwPDB documentation for every tag
Interactive Column Highlighting
Place your cursor on any field name or data value to highlight the entire column. This makes it easy to track columns in dense data tables.
Category Search
Quickly jump to any mmCIF category in the file.
- Command Palette:
Cmd+Shift+P (macOS) / Ctrl+Shift+P (Windows/Linux) → mmCIF: Go to Category...
- Right-Click: Context menu → mmCIF: Go to Category...
AlphaFold / ModelCIF Support
Specialized support for AlphaFold and other structure prediction model files using the ModelCIF dictionary (mmcif_ma.dic).
Automatic Dictionary Detection — The extension reads _audit_conform.dict_name to select the correct dictionary:
- PDBx/mmCIF (
mmcif_pdbx_v50.dic) — Standard experimental structures
- ModelCIF (
mmcif_ma.dic) — AlphaFold, ESMFold, and other predicted structures
pLDDT Confidence Coloring — For ModelCIF files, B_iso_or_equiv values are colored by confidence level:
| pLDDT Score |
Color |
Confidence |
| > 90 |
Dark Blue (#0053D6) |
Very high |
| 70-90 |
Light Blue (#65CBF3) |
Confident |
| 50-70 |
Yellow (#FFDB13) |
Low |
| < 50 |
Orange (#FF7D45) |
Very low |
This matches the standard AlphaFold color scheme.
Color Customization
The extension ships with a default color palette that works well on both dark and light themes, independent of your color theme:
| Token |
Default Color |
Role |
| Category |
#8B8FE8 (Soft indigo) |
Category prefix (e.g., _atom_site.) |
| Column 1 |
#E06C75 (Red) |
First field/value |
| Column 2 |
#98C379 (Green) |
Second field/value |
| Column 3 |
#E5C07B (Yellow) |
Third field/value |
| Column 4 |
#61AFEF (Blue) |
Fourth field/value |
| Column 5 |
#C678DD (Purple) |
Fifth field/value |
| Column 6 |
#56B6C2 (Cyan) |
Sixth field/value |
| Column 7 |
#D19A66 (Orange) |
Seventh field/value |
| Column 8 |
#FF79C6 (Pink) |
Eighth field/value |
| Column 9 |
#7FDBCA (Teal) |
Ninth field/value |
Colors cycle for columns beyond 9.
Customizing Colors
You can override any color in your settings.json:
"editor.semanticTokenColorCustomizations": {
"rules": {
"rainbow1:mmcif": "#your-category-color",
"rainbow2:mmcif": "#your-column1-color",
"rainbow3:mmcif": "#your-column2-color"
// ... rainbow4 through rainbow10
}
}
Installation
- Install from VS Code Marketplace
- Open any
.cif or .mmcif file. All features activate automatically.
Build from Source
git clone https://github.com/N283T/mmcif-rainbow-vscode.git
cd mmcif-rainbow-vscode
npm install
npm run compile
Press F5 in VS Code to launch the Extension Development Host.
Limitations
- File Size Limit: VS Code's internal API limits extensions to files under approximately 50MB. For larger files, rainbow coloring and hover features will be disabled.
Contributing
Issues and Pull Requests are welcome on GitHub.
License
MIT
