Interface Reference

This page lists every control in the editor, area by area. Use it to look up a button you don't recognize. The task-oriented pages explain the workflows; they're linked from each section.

Hover over any icon button in the app to see its name in a tooltip, and press ? to show the keyboard shortcut for each control (see Keyboard Shortcuts).

Start Screen

A new, empty document shows Start a new design with Honeycomb, Square and Freeform buttons. Each opens the New Region panel for that type, where you choose its base plane (see Adding a region). A greyed Wireframe card, marked API preview, is for plugin developers: it creates a wireframe region, and hovering it links to the current status of wireframe support.

Below it, or load an existing design is a drop zone (click to browse). It accepts:

• designs: .fn.json, cadnano .json / .cadnano.json
• plugins: local plugin .zip files

Top Toolbar

On narrower screens (such as an iPad), the toolbar buttons show only their icons. Hover over one, or press ?, to see its name.

Save menu

Save status

Next to the document name, a colored dot and label show the state of the browser working copy:

The ⓘ next to it (Storage info) explains that designs are saved in this browser, not on a server, and whether the browser has granted persistent storage (see Persistent storage). When a save fails, a banner with Retry and Download .json also appears (see When saving fails).

Adding a region

Add Region (or one of its menu items) opens the New Region tool panel:

1. The panel shows the region type.
2. Choose its Base Plane: Top (XY) (normal points up, Z), Front (XZ) (normal points forward, Y), or Side (YZ) (normal points right, X).
3. Click Create type Region Here, or Cancel.

With Plugin dev mode on, Add Region offers wireframe regions too, for developers of routing plugins. See Wireframe Plugin APIs.

Load Cadnano Design as a Region opens a dialog where you drop a cadnano .json / .cadnano.json, choose the same Base Plane options, and click Load. The file becomes a new region in the current part.

Open dialog

Open accepts the same files as the start screen. Each dropped file is listed with an action:

• Foldnano .fn.json: Load opens it.
• cadnano .json: Open creates a new .fn.json document from it; the original .json isn't changed. When a GitHub repository is connected, Add original to current repo folder also stores the original file there. If the file could be either lattice, you're asked whether it is honeycomb or square.
• Plugin manifest or local plugin .zip: shows the plugin's details and an Install button (see Plugins For Users).

Loading from a URL

Opening the editor with ?url=<link to a design file> loads that design directly. A cadnano file doesn't record its lattice; when its helix length fits both honeycomb and square and its crossovers don't settle it, the editor asks. Add &lattice=honeycomb or &lattice=square to the link to answer in advance. It isn't stored in the browser until you click Click to Save Locally in the save status and confirm Save to Browser in Save this design to your browser?. To download a copy instead, use the Save menu exports.

Icon Rail

The narrow column on the far left opens side panels:

Click an active icon again to close its panel.

Viewer Toolbar

The toolbar row below the top toolbar belongs to whichever viewer you last worked in. A badge on its left names that viewer. When the left pane is active, a Plane / 3D toggle switches it between the plane view and the 3D view.

Strand view toolbar

Reset view (arrows pointing inward) fits the strand view back to its default zoom.

Mode holds the tools: Pan, Select, Draw strands, Break strand, Skip bases, Insert bases, Paint oligo, Apply modification, Assign sequence, and Split region. See Editing Tools.

View:

Edit (all act on the current strand selection):

The align buttons work in the Select tool and move free ends only (never ends joined to a crossover). They're enabled only when the move is possible for every selected end at once, and the whole alignment is one undo step. See Aligning ends for which ends move and a worked example.

Length (labeled with the active region's name):

On the right, press ? for help is a reminder of the workspace help (shortcuts plus an explanation of each control).

Plane view toolbar

3D view toolbar

Status chips at the right edge show Simulation running, Relaxed layout stale, Plane selected, and, after a run, the block count and RMS error.

When a design has no assigned sequence, oxDNA export first opens No Sequence Data: unassigned double-stranded positions are filled with random complementary bases, and you choose the base for single-stranded positions (T by default, or A, C, G, Random), then click Export.

See Simulation And Export for the workflows.

Tool Panel

A floating panel on the right shows the options of the current tool or view. Its heading names it: Selection Tool, Paint Tool, Modification Tool, Sequence Tool, Skip Tool, Insert Tool, New Region, Circular Scaffold Map, 3D View Inspector, 3D Overlays, or Reference Mesh.

• Drag the heading to move the panel between the top and bottom of the window, or double-click it to flip position.
• The › button collapses it to a small tab; ‹ expands it again.

The per-tool panels are described on Editing Tools and Selection. The view panels are below.

Circular Scaffold Map

A QC view of how staples bind the scaffold (explained in Selection And Highlighting). Draws each scaffold as a circle, with every staple as an arc or chord between the scaffold positions it binds, a radial bar per double-stranded segment (height = segment length), and histograms of segment length and crossover span.

3D View Inspector

See Views And Regions for plane editing.

Strand View: Rows And Context Menu

• Region header: click to make the region active; double-click to collapse or expand it. The plane icon on the header switches the left pane to 3D, shows the planes, and frames that region's plane.
• VH tag (left edge of each row): drag to reorder helices within the region.
• Cross-region arrows mark connections that continue in another region.
• The status bar at the bottom right shows details of whatever is under the pointer.

Right-click in the strand view opens a context menu:

The copy items are disabled when there's no sequence. Set as Scaffold is how you mark the scaffold explicitly (see Mental Model).

The context menu on a segment.

Status Bar

The strip along the bottom of the editor shows, for a GitHub file:

• the branch name,
• unsaved to GitHub (amber dot) when there are uncommitted changes, or ↓ remote ahead when GitHub has newer commits,
• ? GitHub not checked when Foldnano couldn't check GitHub for newer changes (for example while offline); it checks again by itself when you're back online or return to the tab, or click it to try now. Committing still checks, and shows the conflict options if the file changed,
• the repository and file path, and the short commit SHA,
• Backups; click it to open the design's backups (see Saving And GitHub).

With a repository connected but no file open it shows owner/repo · branch · no file open.

Read-Only Tabs

If the same document is open in another tab, this tab shows This file is open in another tab. Editing is disabled. with a Take back control button. Only Pan stays available until you take control; plugins can still run, but their results can't be applied (see Saving And GitHub).

Error Log

The bug icon in the top toolbar opens Error Log, recent errors from this browser, kept locally for troubleshooting. Each entry can be copied as JSON, or use Copy all as JSON to include them in a bug report. Error notifications also offer a View Details link that jumps to the entry.