Arrange & Align

Once objects are on the canvas, Molkit gives you several ways to line them up: an alignment toolbar that appears on selection, snap guides that fire while you drag, layer-order shortcuts, and keyboard nudging for pixel-level 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, and flip buttons 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.

Molkit treats a connected molecule as a single alignment unit, so aligning a structure with a text label moves them as two items, not dozens of atoms.

Three less obvious controls sit alongside the main buttons:

Align text by dropdown (Box / Baseline / Cap-Height): switches the vertical alignment commands (top, middle, bottom) between bounding-box edges and typographic anchors, so rows of text line up on their baselines or cap heights instead of their boxes. It enables only when the selection is two or more text annotations.
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. Handy for reagent labels above reaction arrows.
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.

The last item you selected acts as the anchor and stays put; everything else moves to match it. This follows the convention used by most design tools, so select the object you want to keep in place last.

Distribute

With 3 or more items selected, the distribute horizontally and distribute vertically buttons space them out with equal gaps between bounding-box edges. The outermost items stay fixed and the items between them shift to even out the whitespace.

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. Flip lives only on the alignment toolbar; there is no menu item or keyboard shortcut for it.

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.

Smart guides

Smart guides are live snap hints that appear while you drag. When a dragged object’s edge or center lines up with another object, a guide line appears and the object snaps into alignment. Guide endpoints carry small marker glyphs showing what matched: an open circle marks the object you are dragging, filled chevrons point at it from the matched object, and a circled-plus appears when the match is a structural anchor such as a molecule’s centerline or a text baseline; on release, a brief flash of the guides confirms the snap committed. When the spacing between objects matches an existing gap, distribution pills appear showing the gap distance, with a count badge when the chain has more matching gaps than are shown. Bond drawing also snaps to standard angles and lengths while guides are on.

Toggle smart guides from View > Smart Guides or with Ctrl+;. They are on by default. To move something freely without turning guides off, hold Alt (or Ctrl) during the drag; snapping is suppressed until you release the key.

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.