The goal of the game is to produce the molecule shown on the right side of the screen. To do that, start by placing some precursor chemicals on the board (use the "PRECURSOR CATALOGUE" button in the bottom-right).

The particle-beam-emitters (AKA "waldos"), numbered 1 through 6, can manipulate atoms in a straight line in front of them. Waldos can initially be rotated and freely placed around the edges of the board, but during operation they cannot rotate and can move only one grid space per cycle.

The first puzzle has you making hydrogen peroxide. To do so, you'll need to join two Oxygen atoms. You could add 2 Water (HOH) precursors to the board, or just 1 since it automatically refills as soon as its grid is empty. That gives you the Oxygen (O) you need, but both of its bonds are filled with Hydrogen atoms (H) so it won't be able to form any new bonds yet. You'll need point a waldo at it, then make it get rid of a Hydrogen using the timeline on the left side of the screen.

The timeline runs from top to bottom and loops after the last instruction, each waldo doing 1 instruction per row (AKA 1 "cycle"). Each column controls its own waldo, as shown by the numbers at the top. Click and drag to rearrange instructions, or box-select and move them as a group. Right-click to delete instructions.

You can click-and-drag the "H-" instruction from the bottom-left into the timeline, but hotkeys are easier: Hold F and click the box under the number of your waldo. Removing a Hydrogen means the Oxygen will be missing a bond, and will immediately form one as soon as it touches any other atom that's also missing a bond. Adding and removing Hydrogen (H+ and H-) lets you form and break these bonds. The bottom-right shows how many bonds each type of atom can have.

Press play (Spacebar) or cycle (Tab) to watch it run. The triple-arrow play button runs it at full speed. Don't be afraid to experiment with new instructions as you unlock them, they're all useful. After making your molecule, use the "Output Target" instruction (hotkey: C) to tell a waldo to send the finished molecule out. This will usually be one of the last instructions in the timeline. Press Esc to save and exit a solution, or to quit the game or change your options. Good luck!

• It's ok if your output isn't the same rotation as the example, but it won't count if it's backwards (ie. molecule chirality matters, but that's only relevant in later puzzles).
  
• After solving a puzzle, you're shown a histogram showing how well you did vs. other players in terms of fewest cycles, instructions, and modules (precursors, waldos, etc.) used. Can you optimize your way to the top?
  
• You can save and load different solutions to the same puzzle. You don't have to optimize for all 3 at the same time.
  
• A good way to make fast solutions is to divide the work evenly between every waldo, while letting them be idle for as few cycles as possible
  
• To make solutions with fewer modules, try to see how much you can do with a single waldo.
  
• To make solutions with fewer instructions, try choosing and arranging precursor chemicals to start as close to the goal as possible
  
• Rotating molecules can often do more work than just pushing or pulling them.