Working with NMR-derived molecular structures often means handling NOE distance restraints that involve pseudoatoms—averaged positions typically used to represent equivalent hydrogen atoms. While helpful from an experimental perspective, pseudoatoms can become a bottleneck during structure refinement, especially when your modeling tools can’t interpret them properly.
This is a common issue for researchers using CYANA-generated distance restraints during structural refinement in molecular modeling environments. Many platforms either require custom scripts or fail to correctly identify pseudoatoms, leading to failed restraints or incorrect minimization outcomes. If you’ve ever found a restraints.log file filled with unassigned restraints or seen expected NOE constraints ignored, you’re not alone.
Molecular Restrainer, a SAMSON Extension developed in collaboration with the Orts Group at the University of Vienna, provides a practical solution out of the box: it builds pseudoatoms on the fly from hydrogen atom positions using standard naming patterns.
Which Pseudoatoms Are Recognized?
Molecular Restrainer interprets pseudoatoms based on official naming conventions common for standard residues. Here’s a quick reference table describing how pseudoatom names are matched:
| Pseudoatom | Parent atoms |
|---|---|
Q |
H1, H2, H3 |
QX |
HX1, HX2, HX3 where X is a letter |
QQX |
HX11, HX12, HX13, HX21, HX22, HX23 |
Partial sets are also accepted: for example, QA may be constructed from just HA2 and HA3 if HA1 is missing. This makes the system flexible—and means you don’t need to stress about having every hydrogen.
Limitations: What About Ligands?
While standard residues are handled well, non-standard residues and ligands may have pseudoatom names that don’t match the conventions Molecular Restrainer expects. This could lead to unmatched restraints.
If that happens, don’t guess. Just check the generated restraints.log file for a list of restraints that could not be applied. This makes it easier to debug and refine your input prior to re-running the minimization workflow.
Why It Matters
Correct interpretation of pseudoatoms ensures NOE restraints are not silently ignored. It increases the fidelity of the minimized structure, especially for models destined for publication or PDB deposition. Molecular Restrainer makes this straightforward by performing this step automatically and transparently—no need for intermediate restraint conversion scripts or external preprocessing tools.
Key Takeaways
- Pseudoatoms are automatically created using standard naming patterns.
- No additional input or pseudoatom files are required—Molecular Restrainer builds them directly from hydrogen positions.
- Restraints involving unrecognized pseudoatoms (e.g., custom ligand names) are logged for easy troubleshooting.
This feature helps eliminate a common source of error in NMR-based structural workflows and keeps the focus on modeling—not formatting.
To learn more, including how to perform full energy minimization of NMR ensembles with NOE restraints, visit the original documentation page: https://documentation.samson-connect.net/tutorials/molecular-restrainer/molecular-restrainer/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here: https://www.samson-connect.net