How to Quickly Select Molecular Paths with a Specific Number of Atoms in SAMSON

When dealing with complex molecular systems, it’s often necessary to focus on specific parts of a model to streamline analysis or editing. For example, you might want to target all molecular paths with more than 100 atoms for further inspection, or isolate a range between 100 and 200 atoms for simulation. In SAMSON, the integrative molecular design platform, this can be done efficiently using the Node Specification Language (NSL).

An often overlooked but powerful feature of NSL is its ability to filter conformation paths based on their number of atoms using the path.numberOfAtoms attribute (short name: p.nat). This simple yet effective tool can save hours of manual selection and help maintain accuracy in selection workflows.

What is the path.numberOfAtoms Attribute?

In SAMSON, the path attribute space refers to conformation nodes. The numberOfAtoms attribute (short name: nat) allows you to match paths that contain a specific number of atoms.

This can be helpful in various scenarios such as:

  • Selecting only large fragments or molecules for batch processing
  • Filtering out small molecular paths for clarity during visualization
  • Setting thresholds for conformational path comparisons

Using p.nat in Practice

Here are the two main ways to use this attribute:

1. Matching Paths with More Than a Certain Number of Atoms

If you’re interested in selecting only those paths that contain more than 100 atoms, type:

This filters all conformation nodes and returns only those with more than 100 atoms, making it easy to isolate more structurally significant components.

2. Matching a Range of Atom Counts

Suppose you’re only interested in paths that contain between 100 and 200 atoms. Use:

This matches paths where the number of atoms lies anywhere between 100 and 200, inclusive.

Troubleshooting Tips

  • Be sure you’re working inside the NSL editor or any interface in SAMSON supporting NSL queries.
  • Remember that p.nat applies only to conformation nodes. If your selection isn’t working, double-check the node types.
  • You can combine this attribute with others, such as p.n (name) or p.selected, for more refined queries.

Why Use p.nat?

Manually inspecting molecular paths is not scalable, especially with large systems. With this attribute, you gain flexible control over your model by using numerical criteria. Whether you’re preparing data for simulations, filtering results, or just cleaning up complex visualizations, this tool lets you specify exactly what you need — no more, no less.

To learn more about this and related attributes, visit the full documentation: https://documentation.samson-connect.net/users/latest/nsl/path/

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

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