Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@figpilot create a contact map figure for PDB 7KMG and run QA"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
figpilot checks a figure the way a reviewer would, before you submit it.
It is a Claude Code skill, an opt-in hook and an MCP server that drive structfig, a toolkit that builds structure-biology figures from HTML pages and measures them against a list of checkable rules.
A skill (skill/figpilot) that knows the six steps: study, one object, two prototypes and a gate, build by page, independent reads, QA. It also knows what never to do: heredocs for HTML, invented palettes, ranges for lists, hover-only legends.
An MCP server (mcp/server.mjs) with seven tools: list_templates, new_figure, build_figure, qa_figure, palette_sample, palette_check, render_structure. They call structfig's scripts, so figpilot carries no copy of them.
A hook (hook/figpilot_hook.mjs) that, after you write a page, reads the QA marks of its last build and says them in one line. It is off until you add it, and silent in any project without a control file.
Related MCP server: Rosetta MCP
git clone https://github.com/danilkotelnikov/structfig
git clone https://github.com/danilkotelnikov/figpilot
cd figpilot
npm ci
node scripts/install-notes.mjsThe last command prints the exact commands for your machine: where to link the skill, the claude mcp add line, the hook entry for settings.json. It runs none of them. You paste what you want.
figpilot finds structfig through FIGPILOT_STRUCTFIG, or the folder ../structfig next to it.
You ask for the contact map of a nanobody and its antigen. figpilot lists the templates, copies contacts into your project with a notes stub, fetches the entry from the RCSB if you allow it, renders it in ChimeraX, builds the page, and runs the marks. Then it hands the PNG, and only the PNG, to a fresh reader and asks three questions. The reader usually finds a problem. You fix it, rebuild, ask again. The notes file keeps the dates and the answers.
Copy figpilot.example.json to figpilot.json in your figure project. It has the same keys as structfig's structfig.example.json: strictness, palette, typeLadder, words, widthMm, review, claimBoundary, chimerax, art, plus two for the hook, hook and hookBlocks. Either file name works for the hook and for structfig's build.
Hook setting | Effect |
| silent |
| a failed strict check exits with code 2 and the reason; otherwise the hook never blocks |
To turn the hook off for good, delete the control file or remove the entry from your settings.
Every argument is checked before it reaches a command or a path.
entry is a four-character PDB code, or the path of a .pdb or .cif file inside your project.
chains takes only the keys that structfig's renderer reads (binder, antigen, light, drop, cdr, light_cdr, seed, sigma, t, assign). Values use letters, digits and _ , . : = + -. A semicolon, space, quote or line break is refused.
key, name and template use letters, digits, _ and -, up to 64 characters.
dir, out, art and the file arguments must lie inside the project folder. That is the folder of the nearest figpilot.json or structfig.json, else the working directory. art, tokens, dir of qa_figure and the palette inputs may also lie inside structfig. Files are written only inside the project folder.
render_structure does not use the network. If the entry is not in structfig's data/pdb, it stops and tells you to pass fetch=true. With fetch=true it downloads the file and its record from the RCSB into data/pdb of the structfig folder.
The hook exits 0 and prints nothing when the control file or its input is malformed.
npm testThey start the server over stdio and call its tools, fire the hook with fake payloads, and compare the skill's copied references with structfig's docs. They need structfig next to figpilot. The test that renders with ChimeraX runs only when STRUCTFIG_CHIMERAX is set.
The skill's references are copies of structfig's docs. After you change a doc there, run node scripts/sync-references.mjs; --check fails if a copy is stale.
Code: MIT, see LICENSE. The files in skill/figpilot/references are copies of structfig documents, which are CC BY 4.0, copied from structfig with attribution. See skill/figpilot/references/LICENSE.md.
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Run protein folding, docking, design and sequence analysis tools, and read their results.
Create scientific illustrations, data charts and flowcharts with your SciFig account.
Create and edit scientific figures, generate data charts, and export editable SVG and PowerPoint.
Protein analysis: ESM-2/ESMC embeddings, mutation scoring, landscape scans, ESMFold structure.
