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Molkit

Your First Molecule

This walkthrough takes you from an empty canvas to a finished molecule, cyclohexanol, in about two minutes. Along the way you will use the ring tool, the bond tool, element relabeling, and undo, then save the file or export an image. If you have not opened Molkit yet, see Accessing Molkit first.

Step 1: Place a ring

  1. Press R to select the ring tool.
  2. Hold Shift and click an empty spot on the canvas. A six-membered ring appears where you clicked. The plain Shift+click places cyclohexane; without Shift, the default six-membered ring is drawn as benzene with alternating double bonds.
  3. If you click and hold instead of releasing right away, dragging rotates the ring around its center before you commit it.

The ring tool can also grow rings off an existing structure: click an atom to attach a ring to it, or click the middle of a bond to fuse a ring onto that edge. You do not need either for this exercise, but they matter as your structures grow. See Ring Tool for details.

Step 2: Draw a bond off the ring

  1. Press B to switch to the bond tool.
  2. Press the mouse button down on one of the ring’s carbon atoms and drag outward. A preview bond follows your cursor.
  3. As you drag, the new bond snaps to 15 degree angle increments and to the standard bond length, so structures stay clean without careful aiming. Hold Alt while dragging to place the bond at any angle, or Shift to draw it at any length.
  4. Release the mouse button. Molkit creates a new carbon atom at the end of the bond.

Two more bond tool behaviors worth knowing: clicking an empty spot creates a lone atom, and clicking an existing bond cycles its order (single, double, triple, back to single).

Step 3: Turn the new atom into oxygen

Carbon atoms are drawn without labels by convention. To make this cyclohexanol, the atom you just added needs to become oxygen.

  1. Press O to make oxygen the active element. You can also pick an element from the toolbar; see Atom Tool.
  2. With the bond tool still active, click the atom at the end of your new bond. Its label changes to O. To show it as OH, turn on Structure, then Display, then Show Implicit Hydrogens (off by default); Molkit then fills in hydrogen counts from standard valence.

Press C to switch back to carbon when you are done. Clicking a carbon atom while carbon is active toggles its label between hidden and visible, which is handy when you want an explicit CH3 at a chain end.

Step 4: Undo a mistake

Press Ctrl+Z to undo your last action and Ctrl+Y to redo it. Both are also in the Edit menu. Every step in this walkthrough is undoable, so experiment freely. To remove a specific atom or bond instead, press E for the eraser tool and click it.

Step 5: Save or export

You have two ways to keep your work:

  • Save the document. Press Ctrl+S or use File, then Save. Molkit documents use the .mkit format, which preserves everything and can be reopened for editing later. See Molkit Files.
  • Export an image. Open the File menu and choose Export SVG or Export PNG. SVG stays sharp at any size and suits web pages and slides; PNG works anywhere an ordinary image does.

That is the full loop: draw, label, fix, save. The same handful of gestures covers most everyday structures.

See also