PyMOL
PyMOL-Claude Integration enables AI assistants to visualize and manipulate molecular structures in PyMOL through a bidirectional communication bridge. Developed by Andre Watson, it implements both a PyMOL plugin that starts an MCP-compatible server and a standalone MCP server script that handles JSON-RPC requests from Claude. The integration allows Claude to execute PyMOL commands, retrieve structural information, edit PDB files, and manage molecular visualizations directly within conversations, making it particularly valuable for structural biology workflows, drug design, and protein engineering tasks that benefit from interactive molecular visualization.
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 2026-09-02.
Scan details: Circle-IR · 2026-09-02 · Appeal
View full trust & usage report →Metadata
- Version
- 1.0.0
- Skill type
- atomic
- Execution layer
- mcp-remote
- Category
- productivity
- Source
- PulseMCP
- Repository
- github.com/nanogenomic/molai/tree/HEAD/FINAL
- Author type
- human
- Last scanned
- 2026-09-02
- Updated
- 2026-09-02
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.