Pretty self explanatory. Press the buttons. Yes you can set the distance of the electrons but you have to go into the code and add a way to do it. 3D overlay is just an effect you can turn off where the gray part looks 3d. It can cover atoms if you have them too close to the edge though, so you can turn it off.
Mostly my code I think if you are wondering what the numbers on positions mean, here. x = 1 2 3 y = 4 5 6 costume = 7 angle = 8 9 10 The numbers are just the character position, so x would be first second third characters, etc definitly don't place a single proton and set pixelated to 110 this is not a coincidence I coded it in
