Editing Tools

All routing and annotation happens in the strand viewer with one active tool at a time. The tool row sits at the top of the strand viewer; each tool has a one-key shortcut and, for most tools, a side panel of options. Switching tools never changes your design; it changes what a click or drag does.

Use the interactive walkthrough below to try each tool on a sandboxed tutorial design, then read the reference for the details.

Export fallback: the toolbar contains pan, select, draw, break, skip, insert, paint, modification, and sequence tools. Select controls target filters; draw creates segments and crossovers; break creates nicks; skip and insert change per-base slot structure; paint recolors oligos; modification changes terminal chemistry; sequence assigns or clears bases.

Tool Reference

Tools with options open a floating tool panel on the right (Select, Paint, Modification, Sequence, Skip, Insert). See Interface Reference for moving and collapsing it.

Strand-view tool row with each tool labeled (Pan, Select, Draw strands, Break strand, Skip bases, Insert bases, Paint oligo, Assign sequence, Split region), with the Selection Tool side panel open beside it.

Draw

Draw is how you lay down DNA and connect it.

• Drag across empty space on a strand row creates a new segment spanning the drag.
• Drag from an existing free end extends that strand.
• Drag between compatible endpoints or crossover sites creates a crossover.

Crossovers are directional and always go 3′ → 5′ (upstream 3′ end to downstream 5′ end). On lattice regions, crossovers can only land on constrained crossover sites; freeform regions allow any compatible end-to-end connection. If a drag wouldn't produce a valid connection, nothing is created.

Break

Click a strand position to split the underlying segment into two pieces, inserting a nick. The two halves keep their bases; the oligo they belonged to may split into two oligos depending on connectivity.

Skip / Insert

These edit the per-base slot structure of a segment, which changes its effective length without moving its endpoints.

• Skip (s): click a position to mark a base as deleted; that position is removed from the emitted nucleotide path.
• Insert (i): click a position to add an extra base between neighboring slots.
• Double-click a position to remove the skip or insert there.

Skips and inserts are applied to both strands of the helix at that position. They can't be placed on a strand end, or on a constrained crossover site (a warning explains why).

The Skip and Insert tools share one panel for the active region:

Skips and inserts directly affect sequence length and every simulation export (see Simulation And Export). Add them before finalizing sequence.

A segment showing an insert marker (numbered loop, one extra base) and a skip marker (red X, a deleted base).

The numbered loop marks an insert of one extra base, which lengthens the strand here. The red ✕ marks a skip, a deleted base that shortens the strand by one position. Both actions change the effective sequence length without shifting the base-pair numbering.

Paint

Paint recolors oligos with the panel's Active color. Clicking a color in the panel only makes it the active color; the paint is applied when you click in the strand view. There are two ways to use it:

• One oligo at a time. Switch to Paint (p), pick a color, then click an oligo. Keep clicking to paint more oligos with the same color.
• Many oligos at once. In Select mode (v), select the oligos first (click, Shift + click, or drag a marquee). Then switch to Paint (p), pick a color, and click anywhere in the strand view. Every selected oligo takes the color in one undoable step, and the selection is cleared. The panel shows how many oligos are selected.

Painting is purely cosmetic: it changes how the oligo is drawn in the strand and 3D views and does not affect topology or sequence.

Paint panel open, showing active color, saved colors, random colors, and a custom color picker.

Modification

Apply the currently selected terminal modification (for example a 5′/3′ chemical modification) to free ends:

• to a clicked free end, or
• to all selected free ends at once.

The panel shows the Active modification and lists:

• Builtin modifications (Thiol, Biotin, Cy3, Cy5), each with its marker color,
• Custom modifications for this design. Click +, enter a Name (for example Azide), pick a Color, and click Add (or press Enter). Hover a custom modification to show its ✕, which deletes it; if it's already used, a dialog says how many ends carry it and removes it from all of them when you confirm.
• Remove mode: clicking an end then clears its modification.

Custom modifications are saved with the design. Modification sites can be surfaced later with the "with modifications" highlight (see Selection).

Modification panel showing the built-in modification list (Thiol, Biotin, Cy3, Cy5) and the Remove mode toggle.

Sequence

Assign or clear bases on clicked strands. What a click targets follows the SCAF / STAP and segment / oligo filter toggles at the top of the panel (c, t, d, o). When you fill a strand, its complementary strand is updated to match.

The panel also shows the scaffold sequence status (✓ or ✗ Scaffold Sequence, see below). Pick one of four actions:

After a fill, the panel reports how much of the input sequence was left over and how many bases were missing, so you can tell whether a preset scaffold was long enough.

Fill mode (radio group at the top of the panel) controls how an action interacts with bases that are already assigned:

Scaffold Sequence Indicator

The scaffold sequence indicator summarizes whether scaffold-labelled oligos have sequence coverage that still matches the current topology. A red state means the assigned sequence may be stale after a topology change (a moved end, new skip/insert, break, or reconnection shifted the nucleotide path). Grey means no oligo is marked as scaffold yet, so there is nothing to track; hover it for a reminder, and right-click an oligo and choose Set as Scaffold. The Sequence panel shows No scaffold set in the same case.

Scaffold Sequence indicator shown side by side in its red/stale state and its green/healthy state.

The same status appears as the S badge in the strand-view toolbar; click it to toggle the scaffold highlight.

Split Region

The Split region tool (r) divides one region into two between helix rows:

1. Choose the tool. Move the pointer over the strand view; the gap between two rows of the same region nearest the pointer is highlighted, with the name the new region will get.
2. Click to split. The rows above the gap stay in the original region; the rows below move into a new region with its own copy of the plane.
3. The tool switches back to Select. Escape cancels without splitting.

Splitting doesn't change any routing. It's useful when part of a design should get its own plane (to move or rotate it separately in 3D) or its own length.