MCPymol

A Model Context Protocol server that lets you drive PyMOL with natural language, enabling structure loading, analytical views, measurements, and protein exploration through AI assistants.

→ chemrich/MCPymol · listed on glama

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// key findings

✅

No credential exfiltration, no sensitive file access, no obfuscation

Static analysis found nothing flowing your secrets to unexpected places.

✅

Open source with a license and README

Anyone can audit the code, the license is declared, and the publisher documents what it does.

// required environment variables

This server reads these from process.env. You'll be asked to provide them before it can run.

configMCPYMOL_PORT— Changing the port. Set before launching both PyMOL and the bridge:

configMCPYMOL_MMSEQS_URL— conservation_view is slow First call hits the ColabFold MMseqs2 API (30 s–few min); subsequent calls for the same sequence hit a local cache If you have an internal MMseqs2 server, set

// full audit trail

The full breakdown of what we checked, the deductions that landed, the network hosts, the dependency advisories, and concrete fix guidance is available to verified publishers.

// improvement guidance — verified publishers only

We have 5 concrete improvements we can share with the publisher of this MCP. Each comes with specific guidance to raise the trust score.

// embed badge in your README

[![M8ven Score](https://m8ven.ai/badge/mcp/chemrich-mcpymol-rhffkr)](https://m8ven.ai/mcp/chemrich-mcpymol-rhffkr)

commit: 3f03bad392b00035294725007faa98b2217f11be

code hash: 7bce6016011ba8ce444dd1282221966ede55e9e9e7eb2bf8611ee5d313da3eed

verified: 6/23/2026, 10:45:23 AM

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