PyMOL Agent

PyMOL Agent is a plugin workflow that combines Fastfold skills with natural-language structure editing. You can run fold or MD workflows, load generated artifacts into PyMOL, and iterate on visualization in one place.

• GitHub: fastfold-ai/fastfold-pymol-agent
• Hosted installer: https://fastfold.ai/pymol-agent/install.sh

Open Source Install

Use this path when you do not already have PyMOL installed, or when you want the standalone Fastfold-managed open source setup.

curl -LsSf https://fastfold.ai/pymol-agent/install.sh | sh

If you already have the target environment and only want the agent:

curl -LsSf https://fastfold.ai/pymol-agent/install.sh | sh -s -- --agent-only

To override the conda environment name:

curl -LsSf https://fastfold.ai/pymol-agent/install.sh | sh -s -- --env-name myenv

Then launch PyMOL from that environment:

conda activate myenv
pymol

Commercial PyMOL Install

If you use commercial PyMOL and prefer Plugin Manager installs, install the plugin zip from GitHub Releases.

Latest release asset:

https://github.com/fastfold-ai/fastfold-pymol-agent/releases/latest/download/fastfold-pymol-agent-plugin.zip

In PyMOL:

1. Open Plugin > Plugin Manager > Install New Plugin.
2. Choose Install from PyMOLWiki or any URL.
3. Paste the plugin zip URL above and fetch it.
4. Open the plugin from the Plugins menu.
5. Install Python dependencies once from the PyMOL command line:

fastfold deps install

You can also download that zip locally and install it through Install from local file.

First Run In PyMOL

After PyMOL opens, run:

fastfold doctor
fastfold setup anthropic <your-anthropic-api-key>
fastfold setup fastfold <your-fastfold-api-key>
fastfold ui

Get keys:

• Fastfold API keys: https://cloud.fastfold.ai/api-keys
• Anthropic dashboard: https://platform.claude.com/dashboard

The setup flow stores your Anthropic key for the agent backend and your Fastfold API key for running Fastfold skills and workflows from PyMOL.

Example Workflow

Use esm1b in Fastfold to run a fold job for my sequence, wait for completion,
load the resulting structure in PyMOL, then show cartoon and color by secondary structure.

Use the chat UI for fold jobs, MD workflows, artifact loading, and iterative structure edits without leaving PyMOL.

You can track submitted jobs in your account dashboard: https://cloud.fastfold.ai/jobs.

Next steps

• Terminal-based research workflows: Agent CLI
• Scripted automation and API usage: SDK Install
• Skill-based agent integrations: Skills