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Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into: radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring in mode 4, approx 1/10 ring diameter in mode 5 appears same as mode 2? Seems to be what Pymol uses when it first opens nucleic acid containing file because any other settings change ends and colors.
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