Skip to content
Molkit

Interface Overview

The Molkit window has six areas. Across the top are the menu bar and the action bar. The tool palette runs down the left side, and the canvas fills the center with a tab bar above it. The element picker sits on the canvas’s right edge, properties panels dock to its right, and the status bar runs along the bottom.

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

  • File creates, opens and saves documents. It imports SVG, MOL/SDF and XYZ files (Import MOL/SDF... is described in MOL and SDF Import), opens Document Metadata and Define R-groups, and holds the SVG, PNG and PDF export dialogs, Batch Export and Page Setup. When the document holds a LaTeX animation, Export LaTeX Animation also appears.
  • Edit has undo and redo, the clipboard commands, Duplicate, Select All, Delete and Clear Canvas.
  • Insert adds images, LaTeX equations, a worked LaTeX solution for animation (Import LaTeX Solution), Plotly charts and structure templates.
  • View controls zoom and fit, the Layers panel, the Named Selections panel, Smart Guides, the grid and its settings, the Single-Key Shortcuts and Single-Pointer Editing accessibility options, and the formula readout.
  • Structure holds the chemistry display options (aromatic display, lone pairs, radicals, bond colors, carbon labels, implicit hydrogens, orbitals), atom numbering, the Orbital Picture submenu, stereo labels, structure validation, Clean Up Structure and Straighten Bonds, Derive View and Set Category for views, resonance form generation, SMILES import and export, Copy IUPAC Name, Copy Structure Description, a spellcheck toggle for text annotations, and Structure Settings.
  • Help opens the keyboard shortcut reference, the command palette, What’s New, the open-source licenses and the About box.

Edit > Clear Canvas removes every structure, annotation, group and animation from the document. It asks for confirmation first, and Ctrl+Z brings everything back.

Below the menus, the action bar repeats common commands as one-click buttons: new, open, save, undo, redo, cut, copy, paste, zoom in and out, and Fit Page, then toggles for the grid, Smart Guides and validation warnings, then XYZ import, templates and a 3D view of the selected molecule. Right-click the grid button to open its settings. See 3D Structure Viewer and Import XYZ.

Every menu command is also in the command palette. Press Ctrl+K (or choose Help > Command Palette…), type part of a command’s name, and press Enter. See Command Palette.

Tool palette

The vertical strip on the left chooses the active tool. The drawing tools are Select, Pan, Eraser, Bond, Ring and Projections. Next come the chemistry annotation tools (Charge, Electrons, Orbital Lobes) and the graphic tools (Arrow, Line, Bracket, Text, Shape, LaTeX Equation). A button near the bottom enters animation mode (Shift+A), and a question-mark button opens the shortcut reference. Hover over any button to see its name and shortcut.

A button with a small arrow has a flyout of variants. The Bond flyout, for example, offers bond orders, stereo bonds and the squiggle line, and the Arrow flyout offers reaction and mechanism arrow types. Single letters switch tools: V for Select, B for Bond, R for Ring, E for Eraser and T for Text. Keyboard Shortcuts has the full list.

Canvas and tabs

The canvas is the drawing surface. The tab bar above it holds one tab per open document; right-click a tab to close or duplicate it. See Tabs, Auto-Save & Recovery.

By default the canvas has no edges. Page Setup can switch a document to fixed pages instead, with a page sorter for reordering them; see Page Setup & Pages. When you select something, an alignment toolbar appears with align, distribute and rotate buttons. Align needs at least two items and distribute at least three; rotate works on any selection. See Arrange & Align.

Element picker

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

Properties panels

Select something and a panel for it docks on the right. Atoms, bonds and annotations use Object Properties; shapes and arrows use Shape Properties; charges and projections have panels of their own. Collapse a panel with the chevron in its header.

Two panels open from the View menu. The Layers panel (F7) manages stacking order and visibility; see Layers & Groups. The Named Selections panel lists saved selections and opens by itself when a document contains some; see Named Selections. A validation panel lists structure warnings after you run Validate Structure.

Status bar

From left to right, the status bar shows:

  1. The active tool’s name. The same spot briefly shows messages such as copy confirmations and auto-save storage warnings, and animation mode and the Match Editor use it for their own status.
  2. The molecular formula and weight (click to copy), with a compound-name lookup beside it.
  3. The structure preset and color scheme indicators. Click either one to switch; see Structure Presets and Color Schemes.
  4. A validation issues badge (click it for the list) and a warnings badge, which appears when a notice such as a missing font needs action.
  5. The zoom controls: slider, zoom percentage, Center View and Zoom to Fit. Click the percentage to type a value. Navigating the Canvas explains each control.
  6. The UI: minus and plus buttons, which make the menus, panels and toolbars smaller or larger without changing the canvas zoom. Ctrl+click either one to reset.

Dialogs and settings

Most settings live in dialogs opened from the menus: Structure Settings (Structure menu) for bond, atom and rendering options, Grid Settings (View menu), and Page Setup (File menu). Press ? at any time for the shortcut reference.

Next: Navigating the Canvas