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Interactive Ramachandran Plot#

Use the Interactive Ramachandran Plot SAMSON Extension to explore and edit protein backbone conformations using φ (phi) and ψ (psi) dihedral angles. This powerful tool lets you validate, select, and manipulate residues directly from the plot - you can use it in your protein-modeling workflows, e.g. for structure refinement.

What Is a Ramachandran Plot?#

A Ramachandran plot shows the energetically allowed regions for backbone dihedral angles (ψ vs. φ) in amino acid residues. It highlights favored and disallowed conformations based on steric and energetic constraints.

Getting Started#

  1. Log into SAMSON Connect.
  2. Visit the Interactive Ramachandran Plot Extension page and click Add.
  3. Restart SAMSON - your extension will be ready to use.

Visualizing a Protein#

Load a Structure#

Open any protein of your choice - this tutorial uses PDB ID 1YRF:

  • Open Home > Fetch.
  • Input 1YRF in PDB or PDB (mmCIF).
  • Click the corresponding Load button.

Open the Ramachandran Plot App#

Open the Ramachandran Plot app via Home > Apps > Biology > Ramachandran plot Ramachandran App icon.

Click Update to generate the Ramachandran plot:

Ramachandran plot

  • Yellow areas - energetically favorable regions.
  • White areas - energetically unfavoured conformations.

Here, all the residues are well placed.

Tabs let you filter residues by category:

  • All
  • General
  • Glycine
  • Proline
  • Pre-proline - residues that are just before a proline in the amino acid chain

Explore Individual Residues#

Click on a dot (e.g., a proline residue):

To visualize one particular residue let's click on it directly on the plot (here with the proline):

Ramachandran plot - Prolines

  • The residue is selected in the viewport.
  • The status bar shows dihedral angles (φ and ψ values):

Status message

Interactive Editing#

Option 1: Drag in the Plot#

  • Drag a point on the plot to update dihedral angles in real time.
  • The 3D structure updates instantly.
  • Press Ctrl/Cmd + Z to undo, e.g., if you're not satisfied with the result.

Option 2: Use the Twister Editor#

  1. Select the Twister editor Twister icon from the left-hand menu in the viewport.
  2. Twist the protein in 3D space and observe the plot update live:

Using Twister

Bonus Challenge - Fixing with Normal Modes#

  1. Reload 1YRF.
  2. Compute the first 10 non-linear normal modes (see Calculating non-linear normal modes tutorial).

  3. Set scaling factor to 1 and shift the first mode fully left:

    Normal Modes Analysis

  4. Use the Ramachandran plot to tweak conformations so all residues fall in favored regions.

This is a powerful exercise to combine global motion and local conformation optimization - valuable for simulation and molecular-design readiness.

Applications in Protein Modeling#

  • Detect strained residues before simulation.
  • Refine homology models by editing outliers.
  • Understand conformational flexibility in active or binding sites.

Need Help?#

Have questions or feedback? Feel free to reach out via the Forum, via e-mail, via the Feedback button in SAMSON, or by directly discussing with us.