An instruction is a command placed in the Reactor to affect an atom, molecule or waldo. An instruction can either apply to a red or a blue waldo.

Various Instructions

There are various types of instructions available to manipulate the atoms and molecules.

It is important to note that you may only place one arrow and one other non-arrow instruction on the same grid square per colour. For example in one square you may have a red left arrow and a red Bond instruction - you will not be able to apply any other red arrows or red instructions. You can however have blue and red instructions in the same grid square, for example in one square you may have a red left arrow and a red Bond instruction, as well as a blue up arrow and a blue sync instruction.

The types of instructions are listed as follows:

"Start" InstructionEdit

These are the beginning points of the reactions, and are where Waldos begin moving from. The rules of use are as follows:
  • There are two Start instructions. One for the red and blue waldos, in each Reactor.
  • These are always present in a reactor, and cannot be created or deleted - although you may not have to always use both.
  • The Start points can be moved to any location on the reactor grid and may be configured to face in any direction.
  • Each Start instruction will begin moving a waldo when the solution is started.

Arrow InstructionsEdit

Arrows- WASD

There are four arrows available (up, down, left and right), which when applied will change the direction of travel for the waldo. The rules are as follows:

  • Arrows can be red or blue and will only affect waldos of the same colour.
  • Only one arrow of a particular colour can be applied to a reactor grid square

( Only 1 red arrow can be applied to 1 grid square. Same with blue. )

Arrow UsageEdit

You want to create a closed cycle to get a circular flow of each waldo.

"In" InstructionEdit

This will insert the designated atom or molecule into the relevant reactor grid square. For example, when a red waldo passes over the red "In Alpha" instruction, the atom or molecule noted in the "Alpha" input area, will be inserted into the "Alpha" section. The rules are as follows:
  • "In" instructions are essential, in order to have atoms and molecules entered into the solution.
  • Atoms and molecules are inserted into the input area according the location shown in left-hand guide box.
  • It is possible to have multiple "In" commands for the path of one Waldo. Note you must ensure that the first atom is moved before the second atom arrives as this will cause a collision.
  • You can have blue and red "In" instructions that refer to either the "Alpha" or "Beta" input atoms/molecules. For example, you could have a blue "In Beta" instruction, and then a red "In Beta" instruction. This will create each of those atoms/molecules in the same location in the "Beta" grid area.

In-out R-F

"Out" InstructionEdit

Out (or Output) instructions are activated when a waldo passes over. This will remove the atoms or molecules from the corresponding Output area (4x4). For example, when a red waldo passes over the red "Out Psi" instruction, any atoms or molecules in the "psi"-output-area (4x4), will be removed and added to the total. The rules are as follows:
  • You may have multiple Out instructions of either colour
  • Any out red or blue Out instruction can refer to either output area.
  • You should ensure that only desired atoms or molecules are present in the desired output area before activating this instruction.
  • Atoms or molecules that are currently being held by a waldo are not affected by this instruction.
  • Molecules that overlap the boundary of the output area are not affected by this instruction.

Grab / DropEdit

Grab-drop E
This is instruction can be set multiple ways- Grab, Drop and Grab/Drop. It is set so that it either attaches an atom to a waldo (Grab), or releases a waldo from holding onto an atom (Drop). If set to Grab/Drop, the waldo will automatically drop the atom or molecule if carrying one, or if the waldo is empty it will pick up and carry.
The rules are:
  • Setting to Grab - the waldos will only pick up atoms at this location, and begin moving them.
  • Setting to Drop - the waldos will release any atoms or molecules at this location.


Rotate G

The Rotate instruction is useful for spinning molecules around. This will allow you to position them so they do not collide with others, or to prepare the correct atom for bonding or unbonding.
The rules are as follows:

  • Rotations can be set to be clockwise, or anti-clockwise.
  • Rotations only move 90 degrees.
  • An atom or molecule affected by a rotation will temporarily stop along its path to carry out the instruction before carrying on. This delay should be taken into account in solutions.
  • There is no benefit in introducing a Rotate instruction to a single atom, apart from adding a delay.


Sync T

This is an instruction to temporarily stop a waldo in its path - until another waldo (of the opposite colour) passes over its own Sync instruction.
The rules are:

  • You can have either no Sync instructions or at least two (one red and one blue). You cannot have one Sync instruction by itself in the solution.
  • You may have odd numbers of pairings of Sync instructions. For example 3 blue Sync instructions and 2 red Sync instructions.


Bond Q

The Bond instruction can be set to + or -. A "+" Bond instructions creates a bond between two atoms or molecules placed over adjacent bonding squares. The Bond instruction does not need to be on the same square with the bonder. If you try to create more bonds than possible for a given atom, nothing happens.

A "-" instruction unbonds bonded atoms in adjacent unbonders. Again, unbonding already unbonded atoms does nothing.


Ctrl H
These instructions (found only in Defense Assignments) will allow a waldo to follow an alternative path depending on whether F1, F2, F3 or F4 is pressed, allowing a reaction to be altered in response to external events.

Ctrl H B-C-activated

The highlighted Control icons "B" and "C" show, that these are activated (switched on) ,
by pressing "F2" and "F3".

Control SwitchesEdit

Ctrl H F1234 B-C-activated

Since switching Controls on/off will work only while time/turns are running, press 1 , 2 , 3 first to start the cycles.

Sense Atom Edit

Sense-atom Y

The Sense atom instruction will allow a Waldo to go along a different path then normal if a selected atom type passes over the spectrometer in Sensor Reactors or Quantum Reactors.

Flip FlopEdit

The Flip Flops direct the passing waldo into one of two directions, altering regularly between passes. By combining several Flip Flops you can, for example, create counters. The Flip Flops aren't introduced until in the seventh "episode", the Atropos Station.


Fuse U

Only available in Fusion Reactors, the Fuse instruction adds the atom on the left of the two-square fusing device to the target atom on the right, increasing the target's atomic number by the atomic number of the added atom. Existing bonds of the target atom are preserved where possible. (If there is no target Atom on the right, nothing will happen.)

See alsoEdit