PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This
PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful integration allows for conversational structural biology, molecular visualization. Exposed over MCP by the pymol mcp mcp server, that capability becomes something an assistant can invoke while it works, not something you go and do afterwards.
Installation goes through your MCP client rather than a global install: point it at mcp on PyPI and it is fetched when the client starts. The copy-paste blocks for Claude Desktop, Claude Code and Cursor are further down this page.
Everything the assistant can do here goes through one of these:
Prerequisites — The Prerequisites tool exposed by this serverAmong the developer tooling options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. Pymol MCP's toolset — Prerequisites — is a fair guide to whether it matches your workflow. It is maintained by vrtejus; worth a glance at recent repository activity before you build anything load-bearing on it.
This entry was verified against Pymol MCP's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.
| Tool | What it does |
|---|---|
| Prerequisites | The Prerequisites tool exposed by this server. |
For example:
```json
{
"mcpServers": {
"pymol": {
"command": "/Users/username/pymol-mcp/venv/bin/python",
"args": ["/Users/username/pymol-mcp/pymol_mcp_server.py"]
}
}
}Configuration as documented by the project. Restart the client after saving.
Kill hallucinated APIs — version-accurate, up-to-date library documentation injected straight into context.
Microsoft's official browser automation server — drive a real browser through the accessibility tree, no screenshots needed.
GitHub's official server — repos, issues, pull requests, Actions and code security, straight from your assistant.
Issue tracking at the speed of conversation — Linear's official hosted server with OAuth and zero install.
Local repository surgery — status, diffs, commits, branches and history for any repo on disk.
Timezone sanity for AI — current time anywhere and correct conversions, without the model doing date math.