Pellaeon

Talk to UCSF ChimeraX in plain English. A chat panel inside ChimeraX that turns what you type into ChimeraX commands, shows every command it ran, and asks before anything destructive.

Install

Pellaeon is on the ChimeraX Toolshed. In ChimeraX, open Tools > More Tools... and press Install next to Pellaeon, or paste this into the command line:

toolshed install ChimeraX-Pellaeon

Open it from Tools > General > Pellaeon. Pick a model provider, paste a key if it needs one, press Test connection, then Save & use. Needs ChimeraX 1.9 or newer. toolshed update ChimeraX-Pellaeon gets later versions.

Newest release before it reaches the Toolshed: paste open https://github.com/tggr-lab/pellaeon/releases/latest/download/install_pellaeon.py into the same command line.

Offline: download the .whl from Releases and run toolshed install /path/to/the/file.whl.

Models

• ChatGPT Plus/Pro account (recommended if you have one): sign in from Settings, no API key. gpt-6-sol has the highest score in the feature comparison (Tested models); gpt-6.1 Sol and Terra are listed too, with a reasoning-level choice in Settings.
• Free, no card: Google Gemini, or Mistral's free tier (fast, needs phone verification).
• Local, private: Ollama on your own computer (gemma4:12b on a 12 GB GPU, qwen3:8b on 8 GB).
• Paid: Anthropic Claude, OpenAI, Mistral Medium, or any OpenAI-compatible server (OpenRouter, Groq, LM Studio).

Keys stay on your computer. How to get a key, and how each model did on our test set: tested models.

What you can do

open the AlphaFold model of ADRB2 and color residue 113 blue what is near the selected residue? compare this with 4ake and show me which contacts are lost color it by ClinVar variants, then by conservation tidy the labels and save a figure with its commands

• Explore a structure: select, inspect neighbours, measure, label. "it" and "the selected" refer to what is open.
• Compare conformations: superpose, residue displacements, lost and gained contacts drawn on the structure.
• Map your data: a residue table, UniProt features, ClinVar variants, ConSurf conservation or AlphaMissense scores, placed in the structure's own numbering with a color key.
• Make figures: publication look, tidy overlapping labels, save the image with a replayable .cxc script and a report: legend, Methods paragraph, sources with release and retrieval date, commands, citations.

Every reply lists the commands it ran, with copy, re-run and a docs link. Closing, deleting, saving and scripts wait for your OK; Stop ends a batch after the running command. Undo (↶) puts ChimeraX back to how it was before the last request.

Membrane proteins get OPM's orientation on request, receptors their GPCRdb structures and inactive/active models, and ConSurf coloring uses its nine grades.

Learn more

• Website and tutorials
• Install guide (providers, privacy, where things are stored)
• Pellaeon and ChimeraX's mcp command: how they differ, and the pellaeon tool ... commands that work from either
• Classic edition for UCSF Chimera 1.x
• Problems: the ? button copies a report (versions, model, the last turns, paths removed) and opens an empty GitHub issue for you to paste and post; Copy chat copies the whole conversation

Citing

Amir, Y. Pellaeon: an AI assistant for UCSF ChimeraX. Zenodo. https://doi.org/10.5281/zenodo.23395411

This DOI covers all versions; each release has its own. GitHub shows Cite this repository from CITATION.cff.

Pellaeon is developed at the Translational Genetics and Genomics Research Laboratory (TGGR), Tel Aviv Sourasky Medical Center.

Development

git clone https://github.com/tggr-lab/pellaeon
cd pellaeon
chimerax --nogui --exit --cmd "devel install \"$(pwd)\""      # install into your ChimeraX

Pure Python, no extra packages. MIT license; bundled ChimeraX and Chimera documentation material stays with its owners, see NOTICE.

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Made by Yam Amir at the TGGR Lab. Named after Gilad Pellaeon, captain of the Chimaera. Not affiliated with UCSF.