When fine-tuning a protein model before simulation, small conformational issues can turn into big problems. A single residue with unusual backbone angles can affect the outcome of minimizations or dynamics runs. But how do you spot and adjust such residues efficiently?
The Interactive Ramachandran Plot Extension in SAMSON offers a highly visual and responsive way to do this — and it works by combining classic visualization with intuitive editing tools.
Diagnosing Problems with the Ramachandran Plot
The Ramachandran plot is a key reference tool in protein modeling. It maps φ (phi) and ψ (psi) dihedral angles for each residue onto a 2D plot, visually highlighting which conformations fall into energetically favorable regions — and which do not.
The Interactive Ramachandran Plot goes a step further: clicking on a dot on the plot not only selects a residue but also highlights it directly in the 3D structure viewer so you can immediately check its context.
Drag and Fix Conformations in Real Time
If you’ve modeled a loop or imported a structure that has clashes or distortions, it’s often a residue or two just outside favorable dihedral ranges that causes trouble. The Interactive Ramachandran Plot lets you fix this directly:
- Just drag the point representing the residue on the plot.
- As you drag, the φ and ψ angles are updated in real time.
- The changes are instantly reflected in the protein’s 3D structure.
Undo support (Ctrl/Cmd + Z) lets you backtrack if a manual edit doesn’t produce the expected result.
This drag-and-drop interaction saves modelers valuable time. Instead of navigating torsion editors or adjusting atom coordinates manually, you get a fast, visual handle on geometry correction.
Keep the 3D Context in View
Every edit via the plot updates the 3D structure, so you can:
- Assess how local changes affect overall geometry.
- See whether clashes are resolved or introduced.
- Refine specific loops or motifs without running a full minimization.
To use this feature:
- Install the Interactive Ramachandran Plot Extension.
- Load a structure (e.g. via Home > Fetch, entering PDB ID
1YRF). - Open the Ramachandran Plot via Home > Apps > Biology > Ramachandran plot.
- Click Update to generate the plot.
- Click a point to select a residue, and then drag it to update the angles.
Beyond Editing: Understanding Residue Categories
The app also comes with filters to view:
- General residues.
- Glycine – flexible due to its small side chain.
- Proline – constrained φ angles from its ring.
- Pre-proline – located right before proline residues.
Each category has different allowed regions in the plot, and the app respects these when evaluating fitness — an important detail during refinement.
Why It Matters
Manual geometry correction is often tedious, especially for beginners. This drag-to-edit feature lowers the barrier. It helps you refine conformations interactively and spot potential problems before committing to deeper analysis — or simulation.
To learn more and walk through detailed steps with screenshots, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.