Protein backbone angles can be shown in a Ramachandran Plot along with probability contours (green lines) from a reference set of well-determined 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. In the example, all helix residues have been selected. Conversely, clicking a dot in the plot will select the corresponding residue in the structure. When the plot has mouse focus, the cursor position (x = φ, y = ψ) is reported under the plot.

BILD format was used in Chimera to annotate the barrel structure of green fluorescent protein with its centroid, major axis (red arrow), and an enclosing cylinder (shown with green hoops). The BILD file green.bild was generated with the python program green.py using the coordinates in green.pdb. Gallery entry courtesy of Mike Ess, Yeast Resource Center, University of Washington. (More samples...)