Quoting Eric Martz <[EMAIL PROTECTED]>: > At 1/14/04, timothy driscoll wrote: > >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. It's also what Jmol b6 branch and CDK uses, which was copied to practice in small molecule organic chemistry... > Along the same vein, absence of charge can be gray, like carbon, the core > of the apolar parts of proteins. CDK has white in the middle, but with some shadowing that's grey... > 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! Not sure what small molecule organic chemists do here, but it indeed makes a lot of sense... Egon
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