Sybyl applies the energy calculations performed in ProTable to the structure and shows the variance in the numbers according to a color scheme. Residues with high energies are red and those of low energies are purple. The same difficulties in the interpretation of these results apply. Rasmol, another protein viewing program, allows one to highlight the protein structures with different colors to show the differences in the groups, the secondary structures, and charge. The BRD structure was colored to show the differences in charge.
High values are blue and low values in red.
This is not a fixed scale so green cannot be assumed to be neutral. Most of the protein is colored red, which indicates a trend in uncharged amino acids. IF was colored to highlight the different secondary structures. The helices are magenta, loops are purple, and all others are white. The same cAR2 model was colored to show the differences in charge.