pymol-mcp

Item: pymol-mcp
Rating: 54
Author: M8ven

Headless PyMOL for molecular visualization, GROMACS/LAMMPS MD trajectories, and clathrate-hydrate cage analysis: H-bond networks, F3/F4 order parameters, and TRACE cage perception + occupancy.

→ wjgoarxiv/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_ALLOW_CODE_EXEC— Typed, safe tools — every argument is schema-validated; the arbitrary-code passthrough is opt-in (=1).

// 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 7 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/wjgoarxiv-pymol-mcp-1e8p3v)](https://m8ven.ai/mcp/wjgoarxiv-pymol-mcp-1e8p3v)

commit: a3d7307f6d2579dc2b0c1df8e0cafc38437de396

code hash: 8a48a7d0fc0aff491ce98369a6b4c1182001ee5ea76912d55fe949f598f6c9ca

verified: 7/8/2026, 8:43:13 AM

view raw JSON →