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I have been using several chemical drawing softwares including MarvinSketch, Jmol, Accelrys DS Visualizer, Avogadro, etc., all of which I have set to CPK colouring. Despite this supposedly common setting I have noticed that fluorine atoms are coloured rather varyingly from software to software. For example, MarvinSketch uses orange, Accelrys uses cyan as does Avogadro and Jmol uses algae green for fluorine atoms. I have tried Googling for the answer but I have only found incomplete tables, aside from on the Wikipedia website but I am dubious as to using Wikipedia for this information due to its reputation for inaccuracy.

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Indeed, this is annoying. Because of this problem, several years ago, one of the Jmol developers and I sat down and worked out a color scheme. It was similar to Accelrys, although we tried to make certain "known colors" match (e.g., rust-like for Fe, golden for Au, etc.)

Certainly, there's been an effort to keep color consistency between Jmol and Avogadro

These colors are open source and available, e.g., through Open Babel

If there are differences between Jmol and Avogadro, I'm sure both the Jmol developers and the Avogadro developers (including myself) would be happy to reconcile them.

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