Instructions are in-game. To make atoms 'bulge' in covalent mode, click and drag the bond button which looks like (O-O) between two atoms so that it's touching both. ALL ATOMS MUST BE IN PLACE BEFORE YOU MAKE ANY BONDS, or else it will glitch and not make any sense! Also, the number of bonds needed to make an atom bulge is the number written on the atom. The negative symbol is ignored in this mode.
Note: To be "scientific", all bonds must be between TWO ATOMS, no more and no less. Keep this in mind and try to complete these ////////////////////////////////CHALLENGES!\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1: Find a way to combine a test tube of HH with one of OO 2: Make test tubes of CHHHH, OO, and OO, then combine them to make carbon dioxide (COO) and water (HHO) 3: Make test tubes of Cyanide (HCN) and the World's Strongest Acid (HF) and combine them to make any one "less dangerous" chemical 4: Use any number of B and FF test tubes to create any number of BBFFF test tubes with nothing left over.