User:Karsten Theis/overall views

To show where negatively or positively charged molecules are bound, 2D-figures sometimes show surfaces colored by an electrostatic potential calculated from the point charges on Asp, Glu, Arg, Lys and - if the charge state is known - His. The common color scheme is blue for positive and red for negative potential (corresponding nicely to the CPK color scheme with blue nitrogen atoms - carrying a positive formal charge - and red oxygen atoms - carrying a negative formal charge). A quick and simple approximation in Jmol is to show the molecule as spacefill, and . (You could also just color the side chain oxygen and nitrogen atoms, but you then ignore charges of disordered atoms missing in the model but present in the protein.) The UvrB protein shown does not exhibit any obvious regions of positive or negative charges.

select protein; spacefill 100%; color silver; select (arg, lys, his) AND sidechain; color blue; select (arg, lys, his) AND sidechain; color blue;