Ramachandran

The Ramachandran analysis plots protein backbone conformations in phi/psi space. It is a natural way to inspect secondary-structure preferences, conformational outliers, and backbone transitions along a path.

Adding the plot

1. Open Path Analyzer.
2. Choose Ramachandran in Observable.
3. Choose a Path.
4. Define a Residue or protein selection.
5. Click Add Scatter.

Inputs

• The selection must contain atoms belonging to protein residues.
• Each valid residue contributes phi/psi points across the path.
• Path Analyzer chooses a suitable background automatically and lets you change it later in card settings.

View

• Scatter: plot phi on the x-axis and psi on the y-axis.

Interactions

• Clicking a point moves the path to the corresponding frame.
• Double-clicking a point selects the corresponding residue in SAMSON.

Tip

• Use a focused residue selection when you care about one loop, motif, or active site.
• Use a broader protein selection when you want a global picture of conformational sampling.
• Ramachandran points are excellent companions to Secondary structure content and RMSD.