Interface Overview

Molkit’s workspace has six regions: a menu bar and action bar across the top, a tool palette on the left, the drawing canvas in the center with a tab bar above it, an element picker on the canvas’s right edge, docked properties panels on the right, and a status bar along the bottom. This page tells you what each region is for and where to find common controls.

The menu bar holds File, Edit, Insert, View, Structure, and Help.

File covers new, open, save, document metadata, importing XYZ coordinates, the SVG, PNG, and PDF export dialogs, and Page Setup.
Edit covers undo, redo, clipboard actions, duplicate, select all, and delete.
Insert adds images, LaTeX equations, Plotly charts, and structure templates.
View controls zoom and fit, the Layers panel, Smart Guides, the grid and its settings, and the formula readout toggle.
Structure holds chemistry display options (aromatic display, lone pairs, implicit hydrogens, atom numbering, stereo labels), structure validation and cleanup, SMILES import and export, a spellcheck toggle for text annotations, and Structure Settings.
Help opens the keyboard shortcut reference, the command palette, the What’s New changelog, and the About box.

Below the menus, the action bar repeats the most-used commands as one-click buttons: new, open, save, undo, redo, cut, copy, paste, zoom, grid toggle, a 3D view of the selected molecule, XYZ import, and templates. See 3D Structure Viewer and Import XYZ.

Tool palette

The vertical strip on the left selects the active tool. Drawing tools include Select, Pan, Eraser, Bond, Ring, and Projections, followed by chemistry annotation tools (Charge, Electrons, Orbital Lobes) and graphic tools (Arrow, Line, Bracket, Text, Shape, LaTeX). A play button at the bottom enters animation mode, and a question-mark button opens the shortcut reference.

Buttons marked with a small arrow have a flyout menu of variants. For example, the Bond tool flyout offers bond orders, stereo bonds, and the squiggle line, and the Arrow flyout offers reaction and mechanism arrow types. Single-letter shortcuts switch tools: V for Select, B for Bond, R for Ring, E for Eraser, T for Text.

Canvas and tabs

The canvas is the SVG drawing surface where you build structures. A tab bar above it lets you keep several documents open at once; right-click a tab for close and duplicate options. See Tabs and autosave for how documents persist. A document can also be paged rather than an infinite canvas, with a page sorter for reordering; see Page Setup & Pages. When two or more items are selected, an alignment toolbar appears with align and distribute buttons (covered in Arrange).

Element picker

A narrow column on the right edge of the canvas sets what the drawing tools place. It lists common elements (C, N, O, H, S, P, halogens), generic R and X labels, and a button that opens the full periodic table. Below the elements are quick buttons for functional groups (OH, NH2, COOH, and more) and abbreviations (Me, Et, Ph), with a toggle that places them as a text label or as expanded structure. See Atom tool for details.

Properties panels

When you select something, a context-sensitive panel docks on the right side. Which panel appears depends on the selection: Object Properties for atoms, bonds, and annotations, Shape Properties for shapes and arrows, plus dedicated panels for charges and projections. Panels can be collapsed with the chevron in their header. The Layers panel (View menu, or F7) manages stacking order and visibility, covered in Layers & Groups, and a validation panel lists structure warnings when you run Validate Structure.

Status bar

The bottom strip shows, from left to right: the active tool name (this readout also flashes transient messages such as copy confirmations and autosave storage warnings, and is taken over by animation mode and the Match Editor for their own status), the molecular formula and weight (click to copy, with an IUPAC name lookup beside it), the structure preset and color scheme indicators, a warnings badge, and zoom controls (slider, center view, zoom to fit, clear canvas). Clicking the preset or color scheme indicator opens a dropup for switching; see Structure presets and Color schemes.

A few status-bar details worth knowing. The zoom percentage is click-to-edit: type a value from 10 to 1000% and press Enter to apply. Center View pans the content into view without changing zoom, while Zoom to Fit also rescales. Clear Canvas asks for confirmation, clears animation states along with the drawing, and is undoable with Ctrl+Z. The warnings badge appears when a persistent notice, such as a missing font, needs action. Full pan and zoom gestures are covered in Navigating the Canvas.

Dialogs and settings

Most configuration lives in dialogs reached from the menus: Structure Settings (Structure menu) for bond, atom, and rendering options, Grid Settings (View menu), and Page Setup (File menu). For fast access to any command, open the command palette with Ctrl+K or press ? for the shortcut reference.