Quick Start

Use this page to get to a first successful run quickly, then move into the deeper product-specific docs.

Agent CLI

Use Agent CLI when you want Fastfold to interpret prompts, choose tools, and execute multi-step workflows from one terminal session.

Fast path (install -> setup -> first run)

uv tool install "fastfold-agent-cli[all]" --python 3.10
fastfold setup
fastfold "Fold this sequence with boltz-2 and show binding pockets: MALWMRLLPLL..."

Everyday quick commands

fastfold            # interactive mode
fastfold doctor     # health checks
fastfold --continue # resume last session

Agent CLI references

• Overview and install: /agents/cli
• Setup and local models (Ollama/OpenAI-compatible): /agents/cli/setup
• Quick usage and prompt examples: /agents/cli/usage
• Interactive slash commands: /agents/cli/interactive-commands
• Skills commands: /agents/cli/skills
• Data/report commands: /agents/cli/data-reports
• Troubleshooting: /agents/cli/troubleshooting

If you want lower-level control for scripts, notebooks, or CI, continue with the SDK path below.

Python SDK and CLI

If you prefer scriptable control and reproducible pipelines, use the SDK and SDK CLI path.

Create an API key

Store the key in FASTFOLD_API_KEY so both the SDK and CLI pick it up automatically.

export FASTFOLD_API_KEY="sk-...your-api-key"

Install the package

Requires Python 3.8+.

pip install fastfold-ai

Run a fold in Python

from fastfold import Client

client = Client()

job = client.fold.create(
    sequence="LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES",
    model="boltz-2",
    is_public=True,
)

results = client.jobs.wait_for_completion(job.id, poll_interval=5.0, timeout=900.0)
print("Status:", results.job.status)
print("CIF URL:", results.cif_url())
print("Mean PLDDT:", results.metrics().mean_PLDDT)
print("Viewer:", results.get_viewer_link())

Run a fold from the SDK CLI

fastfold-cli fold --sequence "LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES" --model boltz-2

On success, the SDK CLI prints the created job ID to stdout.

Move to file-backed and workflow-driven runs

Submit a full job payload file:

fastfold-cli jobs create --payload-file fastfold/examples/fold/job_payload.json

Submit Boltz-style YAML directly:

fastfold-cli jobs from-yaml --file fastfold/examples/fold/boltz2_affinity_input.yaml --model boltz-2

Start an OpenMM workflow from local structure files:

fastfold-cli workflows openmm from-manual-files --pdb ./protein.pdb --pae ./pae.json --simulation-name AF-P00698 --sim-length-ns 10 --box-length 50

Start an OpenMMDL workflow from local topology and ligand files:

fastfold-cli workflows openmmdl from-local-files --topology ./KEAP1kd.pdb --ligand ./IQK.sdf --simulation-name "KEAP1 + IQK" --input-json fastfold/examples/openmmdl/workflow_input.json

Use /sdk for the full recipe set, including OpenMM, OpenMMDL, BoltzGen, generic workflows, webhooks, and report sharing.

PyMOL Agent

If your workflow is structure-first, continue with PyMOL Agent for in-app visualization and chat-driven operations. There are two install paths—pick the one that matches how you run PyMOL.

Open Source install

Use this when you do not already have PyMOL, or you want the Fastfold-managed open source stack (conda + installer script).

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

If PyMOL is already in your environment and you only need the agent:

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

Commercial PyMOL install

If you use commercial PyMOL and prefer Plugin Manager installs, use the plugin zip from GitHub Releases instead of the curl installer:

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

Install via Plugin > Plugin Manager > Install New Plugin, then run fastfold deps install from the PyMOL command line once. Full steps: PyMOL Agent.

Docs and repo

• Guide: PyMOL Agent (open source vs commercial, first run, troubleshooting)
• Repository: fastfold-ai/fastfold-pymol-agent

Next steps

Now that you have a quick path running, use these references to go deeper by integration type.

• SDK install: /sdk/install
• SDK overview and recipes: /sdk
• SDK CLI recipes: /sdk/cli
• Agents overview: /agents
• Agent CLI: /agents/cli
• PyMOL Agent: /agents/pymol
• API Reference: /api
• Available models: cloud.fastfold.ai/models