Quickly Find Molecular Subsets in SAMSON with Folder Attribute Filters

When working with complex molecular systems in SAMSON, structure organization often becomes a challenge. Projects can contain thousands of atoms, dozens of molecules or chains, and rich hierarchical folders. If you’ve ever found yourself toggling through folders trying to isolate specific structures — say, all molecules with fewer than 100 atoms or folders containing charges above a certain threshold — you’re not alone.

Fortunately, SAMSON includes an efficient tool to help molecular modelers filter and query folder content: folder attribute filters in the Node Specification Language (NSL). This feature can be a timesaver, especially when navigating large or hierarchical systems.

🧪 What Are Folder Attributes?

Folder attributes in NSL allow you to target specific folder nodes in your system based on criteria like visibility, atom count, chains, name patterns, and more. For example, if you want to select only folders containing visible elements: f.v true.

🔍 Typical Use Cases Among Modelers

Filter out folders with too many atoms: f.nat < 1000 lets you focus on smaller molecules that might be better suited for a given analysis.
Locate charged structures: Use f.fc > 1 to identify folders with positively charged configurations.
Organize by element composition: For example, to find folders with more than 10 carbon atoms: f.nC > 10.
Skip unnecessary coarse-grained models: f.ncga < 10 can help when you need atomic-level detail only.

📘 Combining Filters

NSL allows combining filters for precise queries. For instance, to find visible folders that contain molecules with fewer than 200 atoms and more than 4 sulfur atoms:

f.v true and f.nat &lt; 200 and f.nS &gt; 4

1	f.v true and f.nat < 200 and f.nS > 4

🎛 Attribute Overview

Let’s highlight some particularly useful attributes:

f.nat – Total number of atoms
f.nC, f.nH, f.nN, f.nO, f.nS – Number of carbon, hydrogen, nitrogen, oxygen, and sulfur atoms, respectively
f.nc – Number of chains
f.nm – Number of molecules
f.fc – Formal charge
f.pc – Partial charge
f.nsm – Number of structural models

📎 Example: Finding Charged Molecules

If your analysis focuses on charged structures, you can quickly isolate all folders with a positive formal charge like this:

f.fc &gt; 0

f.fc > 0

Or target a charge range:

f.fc 6:8

f.fc 6:8

This saves time when dealing with large systems resulting from simulations or imported PDBs.

📈 Why Does This Matter?

Manual exploration of project hierarchies can be time-consuming and error-prone. Using folder attribute filters gives you a fast and scriptable way to zero in on relevant content, especially during tasks like:

Preparing data for docking or simulations
Validating structural content
Generating visuals of specific molecular subsets

Whether you’re analyzing partial charges or narrowing down by molecular size, these filters help you work faster and stay organized.

To dive deeper into the full list of folder attributes and their usage, visit the full documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from www.samson-connect.net.