pulsemcp verified Safe content atomic mcp-remote

Molecule Visualization (ChimeraX, PyMOL)

The molecule-mcp server provides a bridge between AI assistants and molecular visualization software, enabling interaction with PyMol and ChimeraX through the Model Context Protocol. It offers tools to open visualization software, execute commands directly in these applications, and save images of molecular structures. The implementation uses FastMCP to expose these capabilities as tools that can be called programmatically, making it valuable for scientific workflows where molecular visualization and manipulation are needed without leaving the conversation interface.

Cognium trust score

97%

Tier

Verified

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/chatmol/molecule-mcp
Author type: human
Last scanned: 2026-09-28
Updated: 2026-09-28

View source Find related skills

MCP

Resolve Molecule Visualization (ChimeraX, 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

Swap --scope user for --scope project to commit it to .mcp.json.

Your client Same endpoint everywhere; only the config key differs. The full list is in the descriptor.

Claude Desktop · Settings → Connectors → Add custom connector

https://api.skillsregistry.net/mcp

Paste the URL as the connector endpoint. No authentication.

ChatGPT · Settings → Connectors → Create (developer mode) → MCP server URL

https://api.skillsregistry.net/mcp

Authentication: none. Works in chat and deep research — the server exposes the connector search and fetch tools.

Codex CLI · ~/.codex/config.toml

[mcp_servers.skillsregistry]
url = "https://api.skillsregistry.net/mcp"