Quickly Identify Complex Systems with Folder Attributes in SAMSON

When working with large molecular systems in SAMSON, it can be difficult to quickly filter out the folders that match specific structural characteristics—such as the number of atoms, chains, or residues—especially when exploring databases of models or complex molecular assemblies.

Fortunately, SAMSON’s Node Specification Language (NSL) provides a powerful way to query these structures with folder-specific attributes. These attributes help you focus your attention only on parts of your model that match exactly what you’re looking for.

Why folder attributes are useful

Imagine you’re working with a molecular model containing several chains, segments, and molecules. You’re only interested in the molecules with more than 1000 atoms, fewer than 3 chains, and exactly 2 segments. Navigating folders manually is inefficient.

This is where folder attributes like f.nat (number of atoms), f.nc (number of chains), and f.ns (number of segments) become extremely helpful.

Examples of folder attribute filters

Let’s break down a few common queries:

f.nat > 1000: matches folders with structures containing more than 1000 atoms.
f.nc < 3: matches folders with fewer than 3 chains.
f.ns 2: matches folders with exactly 2 segments.
f.nm 5:10: matches folders with between 5 and 10 molecules.

These queries are short, readable, and can be combined for precise filtering. For example:

f.nat &gt; 1000 and f.nc &lt; 3 and f.ns 2

1	f.nat > 1000 and f.nc < 3 and f.ns 2

This will return only the folders that meet all three criteria.

List of available folder attributes

Here are some attribute short names and what they represent:

f.nat: number of atoms
f.nc: number of chains
f.ns: number of segments
f.nm: number of molecules
f.nC, f.nH, f.nO, f.nN, f.nS: number of carbon, hydrogen, oxygen, nitrogen, and sulfur atoms
f.nsg: number of structural groups
f.nsm: number of structural models
f.fc, f.pc: formal and partial charge

Tips for using these filters effectively

Use short names (like f.nc) for faster typing and cleaner queries.
Combine queries using and, or, and not for complex searches.
Use ranges (e.g., f.nat 500:1000) to include models within a specific size.

Whether you’re cleaning your data, preparing a publication, or running large-scale simulations, filtering folders using structural attributes will save you time and reduce errors.

Learn more about the available folder attributes and their usage at the official documentation page: https://documentation.samson-connect.net/users/latest/nsl/folder/

SAMSON and all SAMSON Extensions are free for non-commercial use. Get started by downloading SAMSON at https://www.samson-connect.net.