FigureStyle¶

You rewrite the same lighting, background, cartoon-style, and export commands for every figure? FigureStyle turns that into a one-click template: define lighting, per-secondary-structure cartoon style, coloring (including AlphaFold pLDDT), and export settings once, save it under a name, and apply it to any structure — from the GUI or the command line.

Before you start: preparing your structure¶

FigureStyle styles whatever's already open — it doesn't edit the structure itself.

Prepare the structure first

If you need to crop, mutate, fetch from AlphaFold/PDB, or otherwise prepare a model before styling it, a sibling ChimeraX plugin, ChopChopMF, covers that step. Use it to get the structure into shape, then FigureStyle to style and export the figure.

Finding it in ChimeraX¶

Once installed, FigureStyle adds a button under the Graphics tab of ChimeraX's toolbar:

You can also open it via Tools → General → FigureStyle, or from the command line:

ui tool show "FigureStyle"

The tool panel¶

The tool docks as a panel: a template list on the left, four tabs on the right (Style, Coloring, Image Export, Templates I/O), and Apply to Session / Save always visible at the bottom.

FigureStyle panel open on the Style tab

The Style tab's Cartoon section controls per-type helix/strand/coil shape:

Style tab, Cartoon section

Creating and editing a template¶

Click + in the template list for a blank template, or select one and click Copy to duplicate it under a new name.
Edit settings across Style, Coloring, and Image Export.
Click Save to write your changes back to the selected template — this does not touch your current ChimeraX session.
Click Apply to Session to actually run the template's style on whatever is open right now.

Renaming: change the Name field, then Save — a name collision asks whether to overwrite.

Built-in templates can't be overwritten

Publication White, Dark EMDB, and Minimal Stick are protected — editing one and clicking Save without renaming it shows a warning instead of saving. Click Copy first if you want to build on one of them.

Coloring¶

Coloring tab, Single color mode

Pick a Color mode: None, Single color (optionally restricted to one open chain), By chain (rainbow palette), By B-factor (with a color key), By heteroatom, or AlphaFold pLDDT — colors ligands/waters and the whole structure by AlphaFold's own confidence scale automatically.

Image export¶

Set width/height/supersample/format (PNG, JPEG, TIFF), then click Save Image... to render the current ChimeraX view with those settings.

Transparent background

Only meaningful for PNG/TIFF — JPEG has no alpha channel, so FigureStyle always exports it opaque regardless of the Transparent checkbox.

Templates I/O tab

In Templates I/O:

Export... / Import... — save your whole template list to a JSON file, or load one back in. Same-named templates are overwritten, new names are added alongside your existing ones.
Save as .cxc... / Run .cxc... — turn a template into a standalone ChimeraX script (or run one), no plugin required to use the script afterward.
ChimeraX Built-in Presets — apply one of ChimeraX's own presets directly, independent of your saved templates.

Templates I/O → Export... for a .json file, or Save as .cxc... for a standalone script.
Send that file directly to whoever you want to share it with — they use Import... (or Run .cxc...) to load it in.
To contribute it back for other users to discover, submit the .json or .cxc file either way:
- Open a GitHub Issue or pull request with the file attached, or
- Email it to lukasinscience@gmail.com

Include a short description of what it's for. Accepted submissions get added to the community-templates/ folder in the repo.

Community templates

Browse and download templates other users have submitted: community-templates/ — download the file, then Import... or Run .cxc... as above. Nothing's been submitted yet — be the first.

Command line¶

Templates are created and tuned in the GUI; once saved, every one of them is fully usable from the command line — in a .cxc script, ChimeraX run headlessly (--nogui), or driven by another tool (including an LLM agent controlling ChimeraX).

figurestyle list

Lists all saved template names.

figurestyle info "Template Name"

Prints every field of a template as JSON — useful for inspecting what a template does before applying it.

figurestyle apply "Template Name"

Applies a saved template's style to the current session — useful in scripts or for styling many figures without opening the GUI each time.

figurestyle saveImage "Template Name" path/to/output.png

Applies the template and saves an image in one step.

figurestyle set "Template Name" bgColor #eeeeee showAtoms true atomStyle sphere

Changes one or more fields of an existing template and saves it. Covers the fields you'd tweak most often from a script: lighting, bgColor, transparentBg, silhouettes, silhouetteWidth, cameraMode, showCartoon, cartoonHelixMode, showAtoms, atomStyle, showSurface, colorMode, colorSingle, colorPalette, imageWidth, imageHeight, supersample, imageFormat. For anything beyond this set (fine-grained cartoon xsection/width/thickness per secondary-structure type, B-factor ranges, etc.), edit the template in the GUI.

figurestyle duplicate "Template Name" "New Name"

Copies a template under a new name — handy before set if you don't want to change the original.

figurestyle delete "Template Name"

Deletes a template (built-in templates are protected and can't be deleted this way — copy one with duplicate first).

Citation¶

If FigureStyle helped produce a figure in a paper or presentation, a mention of "ChimeraX-FigureStyle (Lukas W. Bauer)" is appreciated but not required. Machine-readable citation metadata is in CITATION.cff.

License¶

MIT — see LICENSE.txt.

Authors¶

Lukas W. Bauer, with AI-assisted development by Claude (Anthropic).