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I implemented the marching cubes algorithm, and after correcting a dozen errors in my 256 cases, and writing some hole-patching code, it works beautifully! I can mesh the entire ribosome quickly and easily. For example, I meshed the RNA in 1kpj.pdb at 4 A resolution in 8 seconds! I don't know if that's fast for other implementations, but it's good enough for me.