I don't recall if any other well-known mol vis programs color by charge; I'll check it out. as a developer, I usually use lightened shades of blue (positive) and red (negative) to indicate charge.
My impression is that this is perhaps the most common color scheme for charge. Or course it is based on the fact that in proteins, nitrogen (blue) is the most common cation, and oxygen (red) the most common anion.
Along the same vein, absence of charge can be gray, like carbon, the core of the apolar parts of proteins.
To simplify "charge" vs. "apolar" to just two colors, I used gray for apolar and magenta for polar or charged (in PE, Polarity2). The rationale is that if you have only one color for charge, blue plus red = magenta. I mentioned this once to Jane Richardson, and she said she thinks the same way. That confirmed for me that it made sense, since she is one of the great pioneers in protein visualization!
-Eric
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