• 드라이브 PyMOL 일반 영어 — Codex, Claude Code, Cursor 또는 휴대 전화에서.*

**co-pymol**는 MCP 서버로 PyMOL을 턴하는 PyMOL 플러그인이므로 MCP 클라이언트(Codex, Claude Code, Cursor)에서 영어로 구동할 수 있습니다. 시작에 MCP 서버를 회전 - 공식 MCP 파이썬 SDK에 내장 - PyMOL의 자체 파이썬 프로세스 내부, 도구로 pymol.cmd API를 폭발, 그래서 당신은 할 수:

• **Automate 분석 및 시각화 ** 손 대신 에이전트
• 자신의 가치 (pLDDT / ipTM / pTM / PAE)는 mmCIF를 파는 gemmi-backed 메트릭 레이어를 통해 에이전트의 창에
• **자신의 도우미 ** - 사용자 정의 PyMOL 사전 설정 / 분석 기능의 .py에 에이전트를 점하고 그들을 사용하도록 요청
• **SSHFS-mounted 클러스터 경로 이상 작업 ** 평소처럼
• ** 원격 세션을 지원하는 MCP 클라이언트를 통해 휴대폰에서 원격 제어 **

Codex 데모

https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e] [T3]] [T3]] [T3]] [T3]] [T3]] [T3]] [T3] [T3]] [T3] [T3] [T3]] [T3]] [T3] [T3]] [T3] [T3]] [T3]] [T3] [T3] [T3]] [T3] [T3]] [T3]] [T3] [T3]] [T3] [T3]] [T3] [T3] [T3]] [T3] [T3]] [T3] [T3]] [T3] [T3] [T3]]] [T3] [T3] [T3] [T3] [T3] https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e [[T3] https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e]]]]] https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e]]]]] https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e]]]]]]]]

Codex / Claude Code / Cursor의 예 세션:

요구 사항

co-pymol

Drive PyMOL in plain English — from Codex, Claude Code, Cursor, or your phone.

co-pymol is a PyMOL plugin that turns PyMOL into an MCP server, so you can drive it in English from any MCP client (Codex, Claude Code, Cursor) instead of typing PyMOL commands by hand. On startup it spins up an MCP server — built on the official MCP Python SDK — inside PyMOL’s own Python process, exposing the pymol.cmd API as tools, so you can:

• Automate analysis and visualisation with an agent instead of doing it by hand
• Read confidence values (pLDDT / ipTM / pTM / PAE) on an agent’s window via a gemmi-backed metrics layer that parses mmCIF
• Drop in your own helpers — point the agent at a .py of custom PyMOL presets / analysis functions and ask it to use them
• Work over SSHFS-mounted cluster paths as usual
• Remote-control from your phone through an MCP client that supports remote sessions

Codex demo

https://github.com/user-attachments/assets/bbbdbe32-bc59-4446-9bd1-3e4860af022e

An example session in Codex / Claude Code / Cursor:

> Load all the CIF files in /path/to/dir/w/predicted/structures/
[all the structures visible on PyMOL window]
Loaded all structures, sorted by mean pLDDT.

> Which one has the worst ipTM?
model_3 — ipTM 0.41 (others are 0.7+).

> Show me the low-confidence loops on structure_500.
[renders cartoon on PyMOL window, residues 142–168 highlighted, mean pLDDT 38]

Requirements

• PyMOL (a normal desktop install — the plugin installs into PyMOL’s bundled Python, not your system Python)
• An MCP client — Codex, Claude Code, or Cursor 3.12.17 or newer. Older Cursor versions may not refresh the tool list when PyMOL starts after Cursor.
• macOS — that’s all I’ve tested on :/ Linux / conda / non-standard installs should work in principle (the recipe is just “install into PyMOL’s bundled Python”) but these haven’t been tested.

Installing

If you prefer to have a coding agent (Claude Code, Cursor, Codex, etc.) do the install for you, point it at AGENTS.md — it’s the same recipe written for an agent to execute.

1. Clone and install

git clone https://github.com/soo-jeongkim/co-pymol.git
cd co-pymol
/Applications/PyMOL.app/Contents/bin/python -m pip install --user -e .

2. Set up the MCP client you use

Choose exactly one:

# Codex
/Applications/PyMOL.app/Contents/bin/python -m co_pymol setup codex

# Cursor
/Applications/PyMOL.app/Contents/bin/python -m co_pymol setup cursor

# Claude Code
/Applications/PyMOL.app/Contents/bin/python -m co_pymol setup claude

Each command installs the shared PyMOL startup hook and configures only the selected client. The other clients do not need to be installed. The Codex and Claude choices require their existing CLI on PATH; the Cursor choice writes ~/.cursor/mcp.json directly. These commands configure co-pymol for a client —