PyMOL-MCP

Item: PyMOL-MCP
Rating: 69
Author: M8ven

Connects PyMOL to Claude AI for conversational structural biology, molecular visualization, and analysis through natural language.

→ jonathan6620/pymol-mcp · listed on glama

Is this your MCP?

Claim it to get a verified publisher badge, a free copy of our full audit findings, and direct contact for any high-priority issues we find.

Install from

Glama

M8ven verifies MCPs across every public registry — install directly from whichever one you prefer.

// 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.

configPYMOL_MCP_VERBOSE

configPYMOL_MCP_HISTORY— Set =/some/dir to write elsewhere, or PYMOL_MCP_HISTORY=off

configPYMOL_MCP_INSTALLER_NO_RUN

configPYMOL_MCP_LOG_LEVEL— INFO (or DEBUG) in the server's env block to turn logging back on.

// 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 6 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/jonathan6620-pymol-mcp-ba6g7x)](https://m8ven.ai/mcp/jonathan6620-pymol-mcp-ba6g7x)

commit: 7345cecec6f274b9dbac318e1b42b95cdf94cc6b

code hash: 9363b764a85a19254f37b9fa67c63afa1587bfc1b099cfdaf45853b691efbc7e

verified: 7/23/2026, 9:03:50 AM

view raw JSON →