The conventional picture of the retinal group in bacteriorhodopsin involves a quaternary nitrogen atom where the conjugated polyene forms a Schiff base with the terminal side-chain nitrogen in Lys-216 resulting in the nitrogen atom having a positive charge. But semiempirical calculations using PM7 and PM6-D3H4 indicate that not only does the nitrogen atom not have a positive partial atomic charge, the calculated charge is, in fact, predicted to be slightly negative. So what's going on?
The answer is that the nitrogen atom is connected to an extended, conjugated hydrocarbon chain. This can be seen in the Jmol files by clicking on "Specific Script."