What is pymol-mcp?
pymol-mcp is a MCP server by wjgoarxiv that headless PyMOL for molecular visualization, GROMACS/LAMMPS trajectories and clathrate-hydrate cage analysis, including H-bond networks and order parameters. It is listed under Other and has 1 GitHub stars.
| Type | Mcp server |
|---|---|
| Author | wjgoarxiv |
| Repository | wjgoarxiv/pymol-mcp |
| Popularity | 1 GitHub stars |
| Category | Other |
| Security | Low risk (96/100) |
| Rank | #3,134 of 4,418 MCP servers; #497 in Other |
| Last commit | 2026-09-02 |
| Runs | Locally |
| Language | Python |
| Platforms | macOS, Windows, Linux |
Is pymol-mcp safe to install?
pymol-mcp scores 96/100 on the MCPMods security check: Low risk. No checks raised a concern. It passed 5 of 6 checks.
MCP server results come from listing signals: who publishes it, where your data goes and what it can do. The code itself is not scanned yet.
| Check | Result |
|---|---|
| Community-built server | Note |
| Runs on your machine only | Pass |
| No credentials mentioned | Pass |
| Read-only by description | Pass |
| No code execution | Pass |
| Source on GitHub | Pass |
How do I install pymol-mcp?
- Find the launch command. The README says how the server starts (npx, uvx, docker or a remote URL) and which API keys it needs.
https://github.com/wjgoarxiv/pymol-mcp
- Add it to Claude Code. Replace the part after -- with the command from the README. Remote servers use --transport http with a URL.
claude mcp add pymol-mcp -- <command from README> claude mcp add --transport http pymol-mcp <server-url>
- Check it connected. This lists your MCP servers and their status.
claude mcp list
Or ask Claude to set it up
Paste this into Claude Code and it installs pymol-mcp for you:
Add the "pymol-mcp" MCP server from https://github.com/wjgoarxiv/pymol-mcp to Claude Code. Read its README for the launch command and any API keys I need, run claude mcp add, then check that it connects.