Skip to content
Molkit

Your First Molecule

In about two minutes you can draw cyclohexanol: a six-membered carbon ring with an OH group on one carbon. You will use the Ring tool, the Bond tool, an element shortcut and undo, then save the result. Open molkit.com in a new browser tab before you start (see Accessing Molkit).

Step 1: Place a ring

  1. Press R to choose the Ring tool.
  2. Hold Shift and click an empty spot on the canvas. A cyclohexane ring appears, centered where you clicked.

Without Shift, the default six-membered ring is benzene, drawn with alternating double bonds. If you hold the mouse button down instead of releasing it, dragging rotates the ring around its center before it is placed.

Later, when you build larger structures, click an existing atom to attach a new ring to it, or click the middle of a bond to fuse a ring onto that edge. The Ring Tool page covers both.

Step 2: Draw a bond off the ring

  1. Press B to switch to the Bond tool.
  2. Press the mouse button on one of the ring carbons and drag outward. A preview bond follows the pointer.
  3. Release the mouse button. A new bond and a new carbon atom appear at the end of the drag.

While you drag, the bond snaps to 15° steps and to the standard bond length, so it lines up without careful aiming. Hold Alt to draw at any angle, or Shift to draw at any length.

Two other Bond tool clicks are useful from the start. Clicking an empty spot places a single atom, and clicking an existing bond steps its order from single to double to triple and back to single.

Step 3: Change the new atom to oxygen

Carbon atoms are drawn without a label, so the new atom is an unlabeled carbon at the end of the bond. For cyclohexanol it needs to be oxygen.

  1. Press O to make oxygen the active element. If another tool was active, choosing an element also switches to the Bond tool. You can pick elements from the toolbar as well; see Atoms and Elements.
  2. Click the atom at the end of your new bond. Its label changes to O.

A faster route skips the element change: point at the atom and type O. The label changes as you type and is committed when you move the pointer off the atom.

The label reads O, not OH, because implicit hydrogens are hidden by default. To show them, choose Structure > Display > Show Implicit Hydrogens.

When you finish with oxygen, move the pointer away from any atom and press C to go back to carbon. With carbon active, clicking a carbon atom shows or hides its label, which lets you write out an explicit CH3 at the end of a chain.

Step 4: Undo a mistake

Press Ctrl+Z to undo the last action and Ctrl+Y to redo it. Both commands are also in the Edit menu. Every step above can be undone, so try things out.

To remove one atom or bond, press E for the Eraser and click it. See Eraser.

Step 5: Save or export

Press Ctrl+S (or choose File > Save) to save the drawing as a .mkit file. A .mkit file keeps everything editable, so you can open it later and continue. See .mkit Files.

To use the drawing somewhere else, choose File > Export SVG… or File > Export PNG… instead. An SVG stays sharp at any size and suits web pages and slides. A PNG is an ordinary image that any program can show. See SVG Export and PNG Export.

For more structures, try drawing ethanol from a single bond or acetic acid with a double bond to oxygen; the same gestures apply. Keyboard Shortcuts lists every key.

Next: Interface Overview