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

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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

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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.

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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...

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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.

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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
    }
}

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Installation

1. Install from VS Code Marketplace
2. 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