Effortlessly Filter Side Chains in SAMSON with Attribute-Based Selection

Molecular modelers often face a recurring challenge: distinguishing and analyzing side chains in complex molecular structures. Having a clear, attribute-based selection process for side chains can save time and provide more precise insights. If you’ve ever struggled to filter and pinpoint specific side chains with distinct properties, SAMSON’s Node Specification Language (NSL) offers a smart solution.

What Are Side Chain Attributes?

In SAMSON, side chain attributes are defined within the sideChain attribute space, which has the shorthand identifier s. These attributes enable users to describe and filter side chains based on a variety of criteria inherited from broader attribute spaces like node and structuralGroup. By utilizing this language effectively, you can refine your selection with incredible precision.

Key Attributes You Can Use

The attribute space includes several useful identifiers, such as:

  • Visibility Control: Use sc.v (visible) or sc.h (hidden) to quickly determine whether side chains are displayed or not. For instance, you could identify all hidden side chains by querying not sc.v.
  • Structural Analysis: Attributes such as sc.nC (number of carbons), sc.nH (number of hydrogens), and sc.nN (number of nitrogens) allow you to filter side chains by their atomic composition. For example, if you want to focus on side chains with fewer than 10 carbons, you’d use sc.nC < 10.
  • Charge-Based Filtering: Attributes like sc.fc (formal charge) and sc.pc (partial charge) are invaluable for electrostatic studies. For instance, sc.pc 1.5:2.0 will isolate side chains with partial charges in the range of 1.5 to 2.0.
  • Material Ownership: The sc.om (ownsMaterial) and sc.hm (hasMaterial) attributes enable queries like not sc.om to find side chains that don’t own any assigned material.

Practical Example: Identifying Specific Side Chains

Imagine you are working on a protein structure with multiple chains, and you are tasked with isolating side chains that:

  1. Have fewer than 10 carbon atoms (using sc.nC < 10).
  2. Are visible (using sc.v).
  3. Possess a formal charge above 1 (using sc.fc > 1).

By combining these attributes, you can construct a straightforward query using SAMSON’s NSL. This type of precision eliminates manual filtering and saves valuable time.

Why These Filters Matter

For many modelers, being able to define specific groups of side chains quickly is critical for targeted experiments, simulations, or visual analyses. The attribute-driven system in SAMSON provides logical shortcuts, helping you zero in on essential structural elements without redundant trial-and-error steps.

Example table of filtering side chains

Next Steps

This is just the beginning of leveraging SAMSON’s powerful filtering capabilities to streamline side chain analysis. To explore a full breakdown of available attributes and examples, visit the official documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can start exploring SAMSON’s capabilities today by downloading it from SAMSON Connect.

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