The Ramachandran plot function in the Model Panel plots the distribution of amino acid backbone conformations in peptide and protein structures. Each amino acid residue is shown as a dot in a graph of φ vs. ψ, more commonly known as a Ramachandran plot or Ramachandran map. Residues are shown as blue dots, or when selected, as red dots. Conversely, clicking a single dot on the plot will select the corresponding residue in the structure.
Probability contours based on a reference set of high-resolution proteins can be shown on the plot as green lines. The reference set and resulting φ,ψ distributions are described in:
Structure validation by Cα geometry: φ,ψ and Cβ deviation. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Proteins. 2003 Feb 15;50(3):437-50Probability contours can be displayed for different subsets of the amino acid residues in the reference proteins, as indicated next to Show region for:
Close removes the Ramachandran plot. Help opens this manual page in a browser window.