Quickly Find Atoms, Molecules, and Chains in Complex Models

Working with large molecular models can be overwhelming. Whether you’re analyzing a multi-chain protein, a coarse-grained system, or a ligand-binding ensemble, the key to productivity is being able to quickly find what you’re looking for.

This is where the Node Specification Language (NSL) in SAMSON comes in handy. By using structural model attributes, you can express selection criteria such as “show me only models with more than 200 atoms and exactly 2 chains” in a single line.

Why filtering matters

Many molecular modelers spend more time parsing visual interfaces than actually analyzing structures. Especially with large systems, it’s just not efficient to click through different parts of a tree view to find a chain or group of atoms meeting specific requirements.

Instead, try this:

This line selects all structural models with more than 200 atoms and exactly 2 chains. It’s fast, clear, and powerful.

What you can filter

In SAMSON’s NSL, you can filter structural models based on many attributes:

  • sm.nat – total number of atoms
  • sm.nc – number of chains
  • sm.nm – number of molecules
  • sm.nr – number of residues
  • sm.nC, sm.nH, sm.nN, sm.nO, sm.nS – number of specific atoms
  • sm.fc – formal charge
  • sm.pc – partial charge

Each attribute can be matched using direct values, ranges (e.g., 100:200), or logical conditions (e.g., <, >).

Examples from real use cases

  • Find protein chains with fewer than 150 residues:

  • Select structural models with between 8 and 10 structural groups:

  • Detect models with a high total partial charge:

Combining criteria

Selections can be combined using and / or. For instance:

This selects all structural models with more than 10 oxygen atoms and more than 20 hydrogens.

Visibility and selection flags

You can also use sm.v (visible), sm.h (hidden), sm.selected, and selection flags like sm.sf to find elements that are currently selected or visible in the viewport.
This is useful for automating workflows after a manual selection or for hiding unwanted elements.

Conclusion

This filtering system can drastically reduce the amount of time spent navigating complex models. Whether you’re working on small organic molecules or large macromolecular assemblies, learning how to apply filters using attribute fields can be a useful skill for your modeling toolkit.

Explore all available filtering options in the full documentation on Structural model attributes.

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

Comments are closed.