One common challenge when working with NMR-derived molecular structures is ensuring that NOE distance restraints are actually satisfied in the resulting models. While tools for applying restraints exist, it’s often hard to see what’s going on—especially when dealing with multiple conformations or complex protein-ligand systems.
The Molecular Restrainer Extension for SAMSON addresses this issue by providing a unique and interactive way to visualize NOE restraints directly inside your modeling environment—even during energy minimization. This small but powerful feature can help you instantly identify structural issues and interpret outcomes more confidently.
Why Restraint Visualization Matters
When refining NMR structures, it’s not enough to simply apply NOE-derived restraints—you want to know which ones are satisfied and where problems remain.
During structure refinement, a restraint violation might not be immediately obvious if you’re only relying on numerical outputs or log files. Worse, when handling ensembles or structures with non-standard residues or ligands, the complexity increases, making errors more likely.
This is where live, visual feedback makes a real difference. By seeing unsatisfied restraints clearly marked in 3D, you can spot errors, fine-tune parameters, or decide if further editing is necessary.
How It Works in Molecular Restrainer
When you run an energy minimization with the Molecular Restrainer in SAMSON, a specialized interaction model appears in your document. This model doesn’t just control the potential—it also visually represents all loaded NOE restraints as color-coded connections between atoms.
Red = unsatisfied restraint
Green = restraint satisfied
Everything in-between is displayed as gradient shades. This makes it very easy to glance through the structure and detect which regions conform to the NOE data—and which don’t.
Adjusting the Visualization
You can customize how restraints are displayed to your liking:
- Open the Document View in SAMSON and select the interaction model created by the Molecular Restrainer.
- In the Inspector, you can change settings like transparency, radius, and more.
This flexibility helps ensure that the visuals fit your workflow, especially if you’re capturing screenshots for reporting or publication.
When Visual Feedback Becomes Essential
This real-time restraint visualization is particularly helpful in cases like:
- Validating ligand placements in protein-ligand NMR models
- Checking if pseudoatom restraints are correctly interpreted
- Troubleshooting questionable minimization results
- Demonstrating refinement progression during presentations or teaching
Besides, if some restraints can’t be applied (e.g., because an atom is missing or misnamed), they will be listed in the restraints.log file so you can track and address the issue.
Final Thoughts
By integrating live restraint visualization into the refinement workflow, the Molecular Restrainer helps take the guesswork out of NMR model preparation. Whether you’re preparing for Protein Data Bank deposition or optimizing your next design project, having visual clarity on restraint integrity saves time and builds trust in your models.
To learn more, visit the official Molecular Restrainer documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.