Easily Filter Molecular Backbones by Atom Counts in SAMSON

Molecular modelers often need to identify specific structural patterns across large systems. Whether you’re working on large proteins, synthetic polymers, or coarse-grained models, it’s common to need quick answers to questions like: “Which backbones have more than 10 carbon atoms?” or “Which structures are charged or neutral?”

Instead of manually inspecting each component, the Node Specification Language (NSL) in SAMSON provides attribute-based filtering that lets you slice through molecular complexity with concise expressions.

Why Atom-Based Filtering Matters

In large molecular systems, even basic questions like counting atoms can become laborious. For example:

• Identifying charged groups in a ligand-binding site
• Selecting backbones that exceed a certain number of heavy atoms for coarse-graining or simplification
• Filtering out solvent or small capping groups from your system

SAMSON’s bb attribute space lets you express exactly what you want: atom type, count range, charges, and more.

Common Attribute Filters for Backbones

Here are some useful attributes you can use with the bb (backbone) space:

• Carbon atoms: bb.nC — number of carbon atoms
• Hydrogen atoms: bb.nH
• Nitrogen atoms: bb.nN
• Oxygen atoms: bb.nO
• Sulfur atoms: bb.nS
• Total atoms: bb.nat
• Partial charge: bb.pc
• Formal charge: bb.fc

Need a specific subset? NSL offers powerful syntax to query value ranges. For example:

How It Helps in Practice

Imagine working with a large ligand-bound protein and wanting to isolate only the backbone groups that are protonated. Just write:

This instantly surfaces groups that might be extra protonated—helpful in protonation-state-corrected docking.

Pro Tips

• Look for ranges: Try something like bb.nC 10:20 to find medium-sized chains.
• Combine attributes: Use logic. For example, bb.nO > 5 and bb.nH < 10.
• Debug visibility: Use bb.visible or bb.vf to filter out hidden nodes.

Filtering with attributes makes it easier to work with large systems, find interesting fragments, and automate parts of your analysis or design workflow.

You can explore the full list of backbone-related NSL attributes in the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at samson-connect.net.