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After reading a prediction file, ProtoShop creates an initial 3D protein structure by concatenating 3D templates for each amino acid residue and enforcing backbone dihedral angles appropriate for their respective secondary structure types. Initial structure creation only involves concatenation of rigid body transformations, and is instantaneous even for large proteins.
The shown cartoon rendering renders alpha helices as spirals, beta strands as arrows to indicate direction, and coil regions as tubes. Hydrogen bonds between amino acid residues are detected in real-time and rendered as dotted yellow lines.
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