Arrange & Align

A finished reaction scheme usually needs its structures on one baseline, its reagent labels centered over their arrows, and equal gaps between steps. The alignment toolbar, its keyboard shortcuts, smart guides, layer-order shortcuts, and keyboard nudging handle that placement.

Select one or more objects with the Select tool and an alignment toolbar appears near the top-left corner of the canvas, next to the tool palette. It holds the align, distribute, flip, and rotate controls described below. Buttons enable and disable based on what you have selected: align buttons need at least 2 items, distribute needs at least 3, and the flip buttons gray out when only text boxes are selected. Rotation works on any selection. Each button’s tooltip shows its keyboard shortcut.

The toolbar is also shown in animation mode. It keeps its place unless it would overlap the animation toolbar in a narrow window, and then it moves just below it. With two or more animation frames selected, the align and distribute buttons line up the frames instead; flip and rotate are disabled for frames.

A connected molecule counts as one alignment unit. Aligning a benzene ring with a text label moves two items; the ring’s six atoms keep their shape.

Three less obvious controls sit alongside the main buttons.

Align text by (Box / Baseline / Cap-Height) sets how Align top, middle, and bottom treat text. Box lines up the edges of the text boxes, padding included. Baseline lines up the letters: the top and middle of the capitals, and the bottom of the tails on g, p, and y. Cap-Height also uses the top of the capitals and the bottom of the tails, with the middle halfway between the two. Each choice has a tooltip, and the dropdown’s own tooltip names the current choice. It enables only when the selection is two or more text annotations, and it returns to Box when you reload.
Snap Text to Arrow, with text and an arrow or line selected together, snaps each text annotation to the nearest endpoint of the selected arrows, offset by a small standard gap. Use it to seat a label such as H₂SO₄ against the end of a reaction arrow.
Reset Label Orientation returns rotated atom labels to upright. Labels pick up a rotation when you rotate or flip a structure; this button clears it for the selected atoms.

Align

Six alignment commands are available: align left, center horizontally, right, top, middle, and bottom. Select 2 or more items, then click the matching toolbar button or press its shortcut.

Shortcut	Command
`Alt+A`	Align left
`Alt+H`	Align centers horizontally
`Alt+D`	Align right
`Alt+W`	Align top
`Alt+V`	Align middles vertically
`Alt+S`	Align bottom

The object you selected last is the anchor and stays put; everything else moves to match it. Select the object you want to keep in place last, for example with a Shift+click. After a marquee or Select All, which add many objects at once, there is no last object, and the anchor is the last item in the selection’s internal order.

Distribute

With 3 or more items selected, distribute horizontally (Alt+Shift+H) and distribute vertically (Alt+Shift+Y) leave equal gaps between neighbouring objects. The two outermost items stay fixed and the space between them is shared out evenly, so objects of different sizes still look evenly spaced.

Rotate

The rotate buttons turn the selection 90 degrees counter-clockwise (Alt+[) or clockwise (Alt+]). The field beside them takes any angle in degrees from -360 to 360: positive turns clockwise, negative counter-clockwise. Press Enter to apply it; the number stays in the field, so pressing Enter again turns by the same amount. Escape leaves the field.

A rotation is one undo step and uses the same turn as the rotate handle. The pivot is the centre of the selection, so four quarter turns bring it back to where it started. Several selected annotations turn together about that centre, as one block, rather than each about its own centre.

The arrange shortcuts work only while something is selected, and not while a text editor or a text field has the keyboard.

Flip

The flip horizontal and flip vertical buttons mirror the selection across its center. Flipping is chemistry-aware: wedge bonds swap with dash bonds so stereochemistry stays correct, atom labels rewrite to read properly (“OH” becomes “HO” on a horizontal flip), and lone pairs, radicals, and orbitals move to the mirrored positions. To mirror a single substituent in place, use Flip Selection below. The same two commands are on the right-click menu as Flip Horizontal and Flip Vertical whenever something is selected. There is no keyboard shortcut for them.

Flip Selection and Detach Selection

Two more right-click commands work on part of a molecule, using the bonds that attach it to the rest. Select the atoms first, then right-click.

Flip Selection mirrors the selected piece across the bond or edge that attaches it to the rest of the molecule, so a substituent or a fused ring folds to the other side without tearing the structure. Wedges and dashes inside the piece swap. A whole, free-standing molecule is mirrored horizontally instead. If the piece has more than one attachment, Molkit shows a warning and changes nothing.
Detach Selection appears only when the selected atoms are bonded to atoms outside the selection. It cuts the piece free (a shared ring vertex is duplicated so both sides keep a complete ring), nudges it half a bond length down and to the right, and leaves it selected so you can move it. Holding Ctrl while you drag a partial selection does the same thing in one gesture.

Layer ordering

Open the Layers panel from View > Layers Panel or press F7. The panel docks on the right and lists every object on the canvas in stacking order. Hovering a row highlights that object on the canvas, so you can tell rows apart before clicking. The panel, along with grouping and ungrouping objects, is covered in full on the Layers & Groups page.

Select a layer in the panel, then reorder it with the panel’s buttons or the keyboard: Ctrl+] brings it forward one step, Ctrl+[ sends it backward, and Ctrl+Shift+] / Ctrl+Shift+[ jump it to the very front or back. These use Ctrl; the rotate shortcuts Alt+[ and Alt+] use Alt.

Smart guides

Smart guides snap a dragged object into line with the edges, centres, text lines, and spacing of the objects around it, and draw a guide to the item it matched. They also appear while you nudge with the arrow keys and while you drag out a new shape or text box. Toggle them from View > Smart Guides or with Ctrl+;; they are on by default. Hold Alt or Ctrl during a drag to move without snapping. Smart Guides explains what lines up with what, which match wins, and what the two keys do to attached arrows.

Precise size and position

When a shape is selected, the Properties panel on the right shows a Dimensions section with W and H fields in pixels, plus a lock button that preserves the aspect ratio while you edit one value. Images and LaTeX annotations get the same width/height controls with their own ratio locks.

For fine position adjustments, use the arrow keys: a plain arrow key nudges the selection 1 px, Shift+arrow moves 10 px, and Ctrl+Shift+arrow moves 1 screen pixel regardless of zoom level. A nudge never snaps, but with smart guides on it shows the guides the selection now lines up with.