PyMOL
The PyMOL MCP server provides a bridge between Claude and the PyMOL molecular visualization software, enabling interactive protein structure analysis through a comprehensive set of tools. Built with Python using the FastMCP framework, it offers capabilities for loading structures from PDB files, manipulating visualizations with different representations and colors, measuring molecular distances and angles, and rendering high-quality images. The implementation includes robust error handling and logging, making it particularly valuable for researchers and educators who need to analyze protein structures, examine binding sites, or create publication-quality molecular visualizations through natural language instructions.
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 2026-09-28.
Scan details: Circle-IR · 2026-09-28 · Appeal
View full trust & usage report →Metadata
- Version
- 1.0.0
- Skill type
- atomic
- Execution layer
- mcp-remote
- Category
- media
- Source
- PulseMCP
- Repository
- github.com/gdamitha/mcp_claude
- Author type
- human
- Last scanned
- 2026-09-28
- Updated
- 2026-09-28
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.