{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_ve83ntrnrht8","handle":"iflow-mcp-pymol-mcp","url":"https://wellknown.network/agents/iflow-mcp-pymol-mcp","links":{"self":"https://wellknown.network/agents/iflow-mcp-pymol-mcp/record.json","html":"https://wellknown.network/agents/iflow-mcp-pymol-mcp","markdown":"https://wellknown.network/agents/iflow-mcp-pymol-mcp/record.md","api":"https://wellknown.network/api/v1/agents/iflow-mcp-pymol-mcp","status":"https://wellknown.network/api/v1/agents/iflow-mcp-pymol-mcp/status","claim":"https://wellknown.network/agents/iflow-mcp-pymol-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/iflow-mcp-pymol-mcp/claim.json","badge":"https://wellknown.network/agents/iflow-mcp-pymol-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/iflow-mcp-pymol-mcp/history","tools":"https://wellknown.network/api/v1/agents/iflow-mcp-pymol-mcp/tools"},"ard":{"identifier":"urn:air::server:iflow-mcp-pymol-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"iflow-mcp_pymol-mcp","summary":"A simple CLI chatbot using the Model Context Protocol (MCP)","description":"# PyMOL-MCP: Integrating PyMOL with Claude AI\n\nPyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful integration allows for conversational structural biology, molecular visualization, and analysis through natural language.\n\nhttps://github.com/user-attachments/assets/687f43dc-d45e-477e-ac2b-7438e175cb36\n\n## Features\n\n- **Two-way communication**: Connect Claude AI to PyMOL through a socket-based server\n- **Intelligent command parsing**: Natural language processing for PyMOL commands\n- **Molecular visualization control**: Manipulate representations, colors, and views\n- **Structural analysis**: Perform measurements, alignments, and other analyses\n- **Code execution**: Run arbitrary Python code in PyMOL from Claude\n\n## Installation Guide\n\n### Prerequisites\n\n- PyMOL installed on your system\n- Claude for Desktop\n- Python 3.10 or newer\n- Git\n\n### Step 1: Install the UV Package Manager\n\n**On macOS:**\n\n```bash\nbrew install uv\n```\n\n**On Windows:**\n\n```bash\npowershell -c \"irm https://astral.sh/uv/install.ps1 | iex\"\nset Path=C:\\Users\\[YourUsername]\\.local\\bin;%Path%\n```\n\nFor other platforms, visit the [UV installation guide](https://docs.astral.sh/uv/getting-started/installation/).\n\n### Step 2: Clone the Repository\n\n```bash\ngit clone https://github.com/vrtejus/pymol-mcp\ncd pymol-mcp\n```\n\n### Step 3: Set Up the Environment\n\nCreate and activate a Python virtual environment:\n\n```bash\npython -m venv venv\n```\n\n**On macOS/Linux:**\n\n```bash\nsource venv/bin/activate\n```\n\n**On Windows:**\n\n```bash\nvenv\\Scripts\\activate\n```\n\n### Step 4: Install Dependencies\n\nWith the virtual environment activated:\n\n```bash\npip install mcp\n```\n\n### Step 5: Configure Claude Desktop\n\n1. Open Claude Desktop\n2. Go to Claude > Settings > Developer > Edit Config\n3. This will open the `claude_desktop_config.json` file\n4. Add the MCP server configuration:\n\n```json\n{\n  \"mcpServers\": {\n    \"pymol\": {\n      \"command\":…","publisher":{"name":"Edoardo Cilia","url":null},"homepage":null,"repository":null,"version":"0.1.0","license":"MIT","protocols":["mcp"],"tags":["chatbot","cli","llm","mcp"],"pricing":null,"endpoints":[{"url":"pypi:iflow-mcp_pymol-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","license":"pypi","summary":"pypi","version":"pypi","description":"pypi","publisherName":"pypi"}},"derived":{"capabilities":[{"slug":"dev.version-control","name":"Version Control","confidence":1,"provenance":"derived"},{"slug":"dev.package-management","name":"Packages & Dependencies","confidence":0.859,"provenance":"derived"}],"categories":["dev"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"iflow-mcp_pymol-mcp","registry":"pypi","observedAt":"2026-09-15T19:23:34.388Z","publishedAt":"2025-11-21T02:33:38.837948Z","latestVersion":"0.1.0"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"iflow-mcp_pymol-mcp","url":"https://pypi.org/project/iflow-mcp_pymol-mcp/","firstSeenAt":"2026-09-09T20:25:15.957Z","fetchedAt":"2026-09-15T19:22:51.435Z","normalizedAt":"2026-09-15T19:22:51.435Z"}]},"firstSeenAt":"2026-09-09T20:25:15.957Z","updatedAt":"2026-09-15T19:23:34.388Z"}