PellaeonHomeInstallTutorialTested modelsPellaeon and MCPClassic editionGitHub

New Pellaeon is in the ChimeraX Toolshed

Talk to ChimeraX in plain English.

Open structures, inspect residues, compare models, and make figures from a chat panel inside ChimeraX. See the commands Pellaeon runs and copy or reuse them.

toolshed install ChimeraX-Pellaeon

Paste into ChimeraX's command line, or install it from Tools ▸ More Tools… without typing anything. Other ways to install

See it workInstall guide
Typing a request into the Pellaeon panel; ChimeraX opens hemoglobin, colors it, shows the hemes as red spheres and spins it

Three steps

  1. Install the panel. Paste the line above into ChimeraX's command line, or open Tools ▸ More Tools… and press Install next to Pellaeon. Details
  2. Connect a model. Sign in with a ChatGPT account, paste a key for a cloud provider, or point Pellaeon at Ollama on your computer. Local or cloud
  3. Run the built-in test request. A button on the settings page opens ubiquitin and colors it by chain.

Setup steps: install guide. Choosing a local or cloud model: model guidance. With the default confirmation setting, file writes and destructive actions wait for your approval.

How it works

Pellaeon uses your current session and ChimeraX documentation to turn requests into commands. Each command is shown, and errors are returned to the model for correction.

How Pellaeon turns a sentence into ChimeraX commands and checks the result
1 · You type“color the transmembrane helices orange and the rest white”. Typos, “it” and gene names are fine.
2 · ContextWhat is open and selected. The documentation of your ChimeraX version, indexed locally. 147 tutorial workflows, 58 recipes, a list of known model mistakes.
3 · The model plansOllama on your PC, or Mistral, Gemini, Claude or OpenAI. It cannot type into ChimeraX; it can only call tools.
4 · Toolsrun commands · read state · search docs · UniProt lookup · annotate (UniProt, ClinVar) · compare · your tables. Every call is logged.
5 · Safety gateClosing, deleting, saving and scripts stop for an editable OK card. Everything else runs.
6 · ChimeraX runs itPellaeon reads the log: what changed, what failed. An error goes back with the real syntax and a suggestion, and the model retries a bounded number of times.
7 · ReplyCards with every command: re-run, copy, open its ChimeraX docs. Export the chat as a .cxc script.
 error + real syntax → try againnext request
1 · You type“color the transmembrane helices orange and the rest white”. Typos, “it” and gene names are fine.
2 · ContextWhat is open and selected. The documentation of your ChimeraX version, indexed locally. 147 tutorial workflows, 58 recipes, a list of known model mistakes.
3 · The model plansOllama on your PC, or Mistral, Gemini, Claude or OpenAI. It cannot type into ChimeraX; it can only call tools.
4 · Toolsrun commands · read state · search docs · UniProt lookup · annotate (UniProt, ClinVar) · compare · your tables. Every call is logged.
5 · Safety gateClosing, deleting, saving and scripts stop for an editable OK card. Everything else runs.
6 · ChimeraX runs itPellaeon reads the log: what changed, what failed. An error goes back with the real syntax and a suggestion, and the model retries a bounded number of times.
7 · ReplyCards with every command: re-run, copy, open its ChimeraX docs. Export the chat as a .cxc script.
 fix and retry next request

Using Claude Desktop or Cursor with ChimeraX's own mcp command? How the two differ, and how they work together.

Where it fails

The model works from the session state and the log; it does not see the 3D view. Small local models pick the wrong chain, hide what they just showed, or answer a question by running commands. A specific request ("color chain B of #2 red") does better than a general one. Every command is shown, so a wrong one is easy to spot, and Undo takes the last request back. Scores by model are on the tested models page.

Reading a command

Every reply shows the ChimeraX commands it ran. Tap or focus on a part to see what it means.

color #1/A:113 blue

model 1, chain A, residue 113, colored blue

What you can do

Explore a structure

Ask which structures exist for a protein and open the best-resolved one. Select a residue, inspect its neighbours, measure distances, or add annotations.

Residues around a heme group, labelled, with contacts drawn

Compare conformations

Superpose structures and inspect residue displacements and contact differences.

A structure colored by C-alpha shift after fitting, with a color legend

Map your data

Import a residue-score table, check its numbering, and color the structure by value or category.

Ubiquitin colored by a hydropathy column from an imported table, with a color legend

Save figures and views

Export images with their recorded commands and sources. Save views and reuse figure styles.

A publication-style close-up of a histidine side chain next to a heme

See it work

Recorded in ChimeraX with the panel. Choose an example, then play or stop the recording.

Import hydropathy scores and color ubiquitin.76 residues mapped, with a color legend.

Follow this guide · Get the example files · Open full size

Details

Loaded docs/examples/ubiquitin_hydropathy.csv through the panel's Import table action on 1ubq, then used the preview card's Apply to color chain A by the hydropathy column.

All 76 table rows are placed on chain A with 0 positions missing and no reference mismatches, and the structure turns blue-to-red by Kyte-Doolittle hydropathy under a key and title that sit clear of it; the camera does not move, so the colour is the only thing that changes.

Selected commands
color byattribute r:pellaeon_ubiquitin_hydropathy_hydropathy #1 palette blue:white:red range -4.5,4.5 target ac novalue gray
key delete
key blue:-4.5 white:0 red:4.5 pos 0.30,0.075 size 0.40,0.04 fontSize 20
2dlabels create pellaeon_title text "ubiquitin hydropathy (gray = no value)" xpos 0.30 ypos 0.165 size 20 color white
view #1
zoom 0.85

Two editions

The ChimeraX edition is a native bundle with a docked panel (install it); the classic edition drives UCSF Chimera 1.x through its REST server and shows the panel in your browser (classic edition). Both editions share the chat interface and model providers. Table overlays and some analysis tools are ChimeraX-only: see the feature differences.

Privacy

With a local Ollama server, model requests are processed on your computer. Fetching structures and annotations still contacts external databases (PDB, AlphaFold DB, 3D-Beacons, UniProt, ClinVar, ConSurf-DB). With a cloud provider, your request, the list of open models, the current selection, the commands you ran by hand in ChimeraX since your previous request (with their output) and any table you loaded are sent to that provider. Screenshots are shared only when the review-the-view option is enabled in Settings.

Command corrections Pellaeon learns (a refused command and the one that ran instead) stay in learned.json on your computer; sharing them with the project is a button you press, and nothing is sent otherwise. Keys are stored on your computer, never in ChimeraX sessions. Privacy detail, including the free tiers · Where things are stored