BioViewer

A powerful Visual Studio Code extension for visualizing biological structures and electron microscopy maps. Built on Mol*, BioViewer brings advanced molecular visualization directly into your development environment.

✨ Key Features

🗺️ Electron Microscopy Maps: Full support for MRC, MAP, and CCP4 volume files with proper visualization
🌐 Remote SSH Ready: Optimized for remote development with efficient file transfer
📦 Compression Support: Automatic .gz file handling saves bandwidth - especially valuable for remote connections
🧬 Multiple Formats: PDB, mmCIF, and all standard structural biology file formats
🔗 Database Integration: Direct access to PDB, AlphaFold, and EMDB databases

🚀 Installation

Open Visual Studio Code
Go to Extensions (Ctrl+Shift+X / Cmd+Shift+X)
Search for "BioViewer"
Click Install

📖 Usage

Commands (Command Palette: `Ctrl+Shift+P` / `Cmd+Shift+P`)

Command	Description
`BioViewer: Open Structure from Database`	Load from PDB, AlphaFold, or EMDB
`BioViewer: Open Files`	Open selected files in new panel
`BioViewer: Open Folder`	Load all supported files from directory
`BioViewer: Add Files to Current Panel`	Add files to active panel
`BioViewer: Add Folder to Current Panel`	Add all supported files from directory to active panel

Supported Formats

Type	Extensions
Structures	`.pdb`, `.cif`, `.mmcif`, `.mcif`, `.ent`
Volume Maps	`.mrc`, `.map`, `.ccp4`
Compressed	All above formats with `.gz` compression

Quick Start

Right-click any supported file in VS Code Explorer → "BioViewer: Open Files"

🌐 Remote Development

BioViewer is optimized for remote SSH scenarios:

Bandwidth Efficient: .gz files stay compressed during transfer
Smart Decompression: Files decompress in browser, not on server
Large File Handling: Memory-efficient processing of big datasets

⚙️ Requirements

Visual Studio Code ^1.96.2 (for compatibility with Cursor)
Modern web browser (for WebGL support)]

🙏 Acknowledgments

This extension was inspired by molstar/VSCoding-Sequence and builds upon the powerful Mol* molecular visualization library.

Key Dependencies:

Mol* (v4.18.0) - The core molecular visualization engine
PDBe & RCSB PDB - Structural databases
AlphaFold - AI protein structure predictions
EMDB - Electron Microscopy Data Bank

🛠️ Development

git clone https://github.com/shuuul/bioviewer.git
cd bioviewer
npm install
npm run watch    # Development mode
npm run compile  # Production build

📄 License

MIT License - see LICENSE file for details.

🆘 Support

Made with ❤️ for the structural biology community

BioViewer

shuuul

BioViewer

✨ Key Features

🚀 Installation

📖 Usage

Commands (Command Palette: Ctrl+Shift+P / Cmd+Shift+P)

Supported Formats

Quick Start

🌐 Remote Development

⚙️ Requirements

🙏 Acknowledgments

🛠️ Development

📄 License

🆘 Support

Commands (Command Palette: `Ctrl+Shift+P` / `Cmd+Shift+P`)