PDF Navigator MCP

A comprehensive Model Context Protocol (MCP) server for PDF reading, navigation, and text search with cross-platform PDF viewer integration. Built on PyMuPDF (MuPDF), exposed through MCP so the dependency stays isolated from your project environment.

Why this exists

Claude Code's built-in Read tool can open PDFs directly, so it's fair to ask whether this server is still needed. It is — but for a narrower reason than it used to be. The built-in reader has two limitations that this server is designed around, and a third tool (poppler's pdftotext) doesn't fill the gap either:

The built-in `Read` tool renders each PDF page as a raster image. Two consequences for scientific papers:

• It's token-expensive and doesn't scale. A figure-heavy 25-page paper is ~25 page-images; reading it whole burns tens of thousands of image tokens and crowds out the rest of the conversation. You can cap it with a pages range (and recent versions require one past ~10 pages), but only if you already know which pages you want.
• Image text isn't searchable. You can't search across pixels. To find where a paper discusses, say, "survivorship bias," you'd read pages as images until you spot it — the exact behavior that fills up context.

Poppler's `pdftotext` is cheap and searchable but mangles the content scientific papers are made of:

• Inline math breaks. Combining marks detach from their base — e.g. p̃(x;t) comes out as a stray ~ on its own line, split from p(x;t).
• Multi-column layout scrambles. Default mode drags in running headers and can reorder text; -layout glues the two columns horizontally so every line reads left-column … right-column, destroying reading order and breaking any phrase search that spans a column.

This server uses MuPDF's `get_text()`, which preserves reading order across columns and keeps inline math intact, and exposes it as cheap, searchable text plus structure/outline navigation. The intended division of labor:

Features

• PDF text extraction - Read full PDFs or specific pages/ranges
• PDF structure analysis - Extract table of contents and page summaries
• Text search with location - Find text and jump to results
• Direct PDF navigation - Open PDFs to specific pages
• Cross-platform PDF viewers - Supports Skim, Zathura, Evince, and more
• MCP integration - Works with Claude Code and other MCP clients
• No dependency issues - PyMuPDF isolated in MCP server environment

Installation

# Install with pipx (recommended)
pipx install git+https://github.com/matsengrp/pdf-navigator-mcp.git

# Or install in current environment
pip install git+https://github.com/matsengrp/pdf-navigator-mcp.git

Claude Code Integration

Add to your ~/.claude.json:

{
  "mcpServers": {
    "pdf-navigator": {
      "type": "stdio",
      "command": "pdf-navigator-mcp"
    }
  }
}

Usage

In Claude Code, you can:

• "Read the abstract from paper.pdf" → Extracts and shows text content
• "What's the table of contents for paper.pdf?" → Shows PDF structure
• "Read pages 5-10 of paper.pdf" → Extracts specific page range
• "Search for 'parameter efficiency' in paper.pdf" → Finds text and locations
• "Open paper.pdf to page 5" → Opens PDF viewer to specific page

MCP Tools

Reading Tools

• read_pdf_text(file_path, start_page, end_page) - Extract text from page range
• read_pdf_page(file_path, page_number) - Extract text from single page
• get_pdf_structure(file_path) - Get table of contents and page summaries
• get_pdf_info(file_path) - Get document metadata

Navigation Tools

• search_pdf_text(file_path, query) - Search text and return locations
• open_pdf_page(file_path, page_number) - Open PDF viewer to specific page
• search_and_open(file_path, query, result_index) - Search and open to result

Supported PDF Readers

• Skim (macOS) - skim:// URL scheme
• Zathura (Linux) - --page argument
• Evince (Linux) - --page-index argument
• SumatraPDF (Windows) - -page argument
• Adobe Acrobat (Cross-platform) - /A page=N argument

Configuration

Configure your PDF reader in ~/.pdf-navigator-config.json:

{
  "pdf_reader": "skim",
  "reader_path": "/Applications/Skim.app"
}

Development

git clone https://github.com/matsengrp/pdf-navigator-mcp.git
cd pdf-navigator-mcp
pip install -e ".[dev]"

License

MIT License