PyMOL
PyMOL MCP Server enables AI assistants to interact with the PyMOL molecular visualization software through a socket connection. Built by Vishnu Rajan Tejus, it provides a comprehensive set of tools for molecular visualization, viewing operations, file handling, and structural analysis. The server parses natural language commands into PyMOL-compatible Python code, executes them via a socket connection, and returns the results. This implementation is particularly valuable for researchers and scientists who need to manipulate and analyze molecular structures directly within their AI assistant conversations without switching contexts.
Composite of vulnerability cleanliness, spec conformance, provenance, stability, and usage signals — scanned and weighted by Cognium. Human and agent signals are tracked separately. Last scanned 2026-09-19.
Scan details: Circle-IR · 2026-09-19 · Appeal
View full trust & usage report →Metadata
- Version
- 1.0.0
- Skill type
- atomic
- Execution layer
- mcp-remote
- Category
- search
- Source
- PulseMCP
- Repository
- github.com/vrtejus/pymol-mcp
- Author type
- human
- Last scanned
- 2026-09-19
- Updated
- 2026-09-19
Use via MCP
Resolve PyMOL from your agent
Streamable HTTP transport at https://api.skillsregistry.net/mcp. No auth for read tools. Discovery: .well-known/mcp.json.
One command in your shell — Claude Code wires it up and verifies the connection. Run /mcp in any session to confirm.
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp--scope user for --scope project to commit it to .mcp.json.