ChatMol

chatmol-streamlit

Streamlit interface for ChatMol’s Agentic Molecular Visualization (AMV).

Overview

This app runs a Streamlit GUI that lets you interact with an LLM-powered PyMOL agent. The agent can:

• Generate PyMOL command sequences from natural-language instructions.
• Execute commands in a running PyMOL GUI session.
• Produce a publication-quality view analysis from a rendered PyMOL screenshot.

Requirements

• Python 3.10+ recommended
• PyMOL (open-source build)
• streamlit (tested with 1.35.0+)
• openai Python SDK
• chatmol package at here

You can install the main dependencies with conda/pip:

conda install -c conda-forge pymol-open-source
pip install streamlit==1.35.0 openai chatmol

Environment variables

The app expects one or more API key environment variables. By default the UI is configured to use OPENAI_API_KEY for all models. Set it before starting Streamlit:

export OPENAI_API_KEY="sk-..."

If you prefer different env var names for different model roles (PyMOL commands, view analysis, agent) you can change them in the sidebar at runtime — the app lets you specify the name of the environment variable to read for each role.

Running the app

From the chatmol-streamlit directory run:

streamlit run app.py

The Streamlit sidebar contains a Model & API settings section where you can:

• Choose model names for PyMOL commands, View analysis, and the Agent.
• Set the base URL for each model (default: https://api.openai.com/v1).
• Set the environment variable name that stores the API key for each model role.

Changes are applied immediately for new requests.

Example prompt

Try the test prompt shown in the sidebar (also used in the app):

Highlight aromatic sidechains of 1pga and prepare to scientific publication level.

When you submit a prompt the app will display assistant messages in the chat area and show the latest screenshot.png produced by PyMOL.

Troubleshooting

• If you see “Environment variable ‘… is not set’” errors, export the API key env var specified in the sidebar (default OPENAI_API_KEY).
• If PyMOL doesn’t start, ensure pymol-open-source is installed and that chatmol’s start_pymol_gui() works on your platform.
• The app saves a screenshot as screenshot.png in the working directory — check permissions if saving fails.

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