Agent-safe MCP server exposing MolCompose figure commands in UCSF ChimeraX
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# molcompose-mcp <p align="center"> <a href="https://pypi.org/project/molcompose-mcp/"><img alt="molcompose-mcp on PyPI" src="https://img.shields.io/pypi/v/molcompose-mcp?color=12A08C&label=molcompose-mcp&logo=pypi&logoColor=white"></a> <a href="https://pypi.org/project/molcompose-mcp/"><img alt="Supported Python versions" src="https://img.shields.io/pypi/pyversions/molcompose-mcp?color=4477AA&logo=python&logoColor=white"></a> <a href="https://pepy.tech/projects/molcompose-mcp"><img alt="PyPI downloads reported by Pepy" src="https://api.pepy.tech/badge/molcompose-mcp"></a> <a href="https://github.com/ChiaChunL/MolCompose/actions/workflows/unit-tests.yml"><img alt="CI" src="https://github.com/ChiaChunL/MolCompose/actions/workflows/unit-tests.yml/badge.svg"></a> <a href="https://github.com/ChiaChunL/MolCompose/blob/main/LICENSE"><img alt="BSD-3-Clause" src="https://img.shields.io/badge/licence-BSD--3--Clause-7B7BD8"></a> </p> **Download statistics:** [Totals (Pepy)](https://pepy.tech/projects/molcompose-mcp). These are package downloads, not unique users or MCP calls. An MCP stdio server for protein-interface analysis and molecular visualization in UCSF ChimeraX. Agents use the same MolCompose commands as the graphical panel. ## Installation Requires Python 3.11+, ChimeraX 1.12 and the [MolCompose bundle](https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxmolcompose). Install the latest published bridge: ```bash python -m pip install --upgrade molcompose-mcp ``` This README describes MCP **0.1.2** with bundle **0.1.3**, not yet published. For this checkout, run `python -m pip install ./mcp` from the repository root and install the matching bundle using the [checkout instructions](https://github.com/ChiaChunL/MolCompose#this-checkout). ## In the MolCompose Agent tab Open **Tools → Structure Analysis → MolCompose**, then select the **Agent** tab. Select an installed, signed-in Codex or Claude Code CLI, then ask a question. The tab starts the local bridge …
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