caDNAno - Tool & Button Reference

caDNAno Tool Button Reference

*Slice Panel Buttons*
icon	name	function
	Edit Tool	Click a helix in the Slice Panel to add scaffold at the current position of the Slice Bar. Shift+Click an existing helix to add staple sequence at the current position of the Slice Bar.

	Zoom Tool	Click to zoom in. Shift+Click to zoom out.

	Move Tool	Click+Drag to reposition the Slice helices.

	First-Slice Button	Click button to move Slice Bar to left-most position.

	Last-Slice Button	Click button to move Slice Bar to right-most position.

	Renumber Button	Click button to renumber helices according to their current order in the Path panel.

	Delete-Last Button	Click button to delete the highest-numbered helix. All crossovers must be removed before deletion is allowed.

*Path Panel Buttons*
icon	name	function
	Edit Tool	Click on a crossover to add or remove. Click+Drag on a breakpoint to reposition. Shift+Click on one of two adjacent breakpoints to ligate a nick. Alt+Click on a breakpoint to move breakpoint to its boundary. Alt+Shift+Click on Slice Bar to move all breakpoints to their respective boundaries.

	Zoom Tool	Click to zoom in. Shift+Click to zoom out.

	Move Tool	Click and Drag to reposition the Path canvas. Tip: use arrow keys ← ↑ ↓ → to avoid switching back and forth to this tool.

	Break Tool	Click to install a 3' nick in scaffold or staple.

	Erase Tool	Click to remove continuous stretch of scaffold or staple (up to any breakpoint or crossover).

	Force Crossover Tool	Click to once to select start position, then click again to select end position. Confirm in dialog box to install a non-standard crossover.

	Loop Tool	Click on a scaffold strand to install a loop, which causes extra scaffold (and optionally staple) bases to be included at a that position. Click on a staple strand to install a specific sequence. Double-Click with Edit Tool to remove a loop.

	Skip Tool	Click on a scaffold position to install a "skip", which causes scaffold and staple sequence to not be installed at the specific position. Double-Click with Edit Tool to remove a skip.

	Paint Tool	Click on a staple to set to selected color. Use color picker to select specific a color. Use keyboard shortcut "p" to cycle through colors.

	AutoStaple Button	Click to install a default set of staples. It is best to complete the scaffold design before using the AutoStaple button. Note: Staples can be installed manually using the Slice Panel Edit Tool.

	Add Sequence Tool	Click on a scaffold 5' breakpoint to apply a scaffold sequence to a design. Sequences are not currently stored, so this tool must be used whenever an existing design is loaded. M13 scaffold hairpins are highlighted when sequence is applied.

	Export SVG Button	Click to export an SVG diagram of the path panel. Sequences will be included if previously applied with the Add Sequence Tool.

*Render3D Panel Buttons*
icon	name	function
	Zoom Button	Click to zoom in. Shift+Click to zoom out.

	Move Tool	Click+Drag to reposition the 3D model. Unselect the tool to return to Examine mode.

	X3D Export Button	Click to export an X3D cylinder model of the scaffold arrangement.

caDNAno Tool Button Reference

Notes