VAMD — molecular viewer

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Representation

"Trace" is a thin Cα tube. "New 3D Cartoon" renders real secondary structure — coiled ribbon through alpha helices, flat arrows through beta sheets, thin tube through loops — the classic PyMOL/VMD look. "Ribbon" is a flat, constant-width strand that ignores secondary structure. Fetching or loading a real protein (e.g. PDB ID 1AKI) automatically switches to New 3D Cartoon with secondary-structure coloring.

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