Ramachandran Plot

The Ramachandran Plot tool shows the backbone dihedral angles φ (phi) and ψ (psi) of the residues of a protein, either for the current frame or for every frame of a trajectory. Each protein residue with N, CA and C backbone atoms is analyzed, and the points are colored by category: General, Glycine, Proline and Pre-proline. The shaded regions mark the usual areas of β-sheet, right-handed (αR) and left-handed (L) helices, and the region allowed for glycine.

To open the tool: Main Menu > Analysis > Ramachandran Plot (Figure 1).

• System / Object: the structure or trajectory.

• Limit to current viewer selection: only plot the residues with at least one atom selected in the 3D view. φ and ψ are still computed with the full backbone of each residue, including its neighbors.

• Use all trajectory frames: off (default): only the current frame is plotted. On: every frame in the range contributes one point per residue, giving a scatter over the sampled conformations (φ and ψ are never averaged across frames).

• Frames from / to and Step Size: the frame range when all frames are used.

• Save results to text file: writes a tab-separated file (chain, residue, residue number, category, frame, φ, ψ).

Click Run. The plot is drawn in the same window; hovering over a point identifies the residue and frame. Hide settings gives the whole window to the plot, and Export PNG... saves it as an image.