Fastfold PyMOL Agent

Fastfold PyMOL Agent is a PyMOL plugin 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: http://fastfold.ai/pymol-agent/install.sh

Quick install

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

Agent-only mode (assumes PyMOL already installed):

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

Custom conda environment:

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

First run in PyMOL

After install:

conda activate myenv
pymol

Then in the PyMOL command area:

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

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.

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

Next steps

• Full CLI research workflows: Fastfold Agent CLI
• Scripted automation and API usage: Python SDK
• Agent skills guide: Skills