Tips for Filtering Structural Models Using SAMSON Attributes

When working on molecular modeling projects, quickly isolating and analyzing specific structural models can streamline workflows and enhance productivity. SAMSON, the integrative molecular design platform, makes this process intuitive through its robust set of structuralModel attributes. These attributes allow modelers to filter and manipulate structural models based on various properties such as the number of atoms, chains, or residues, as well as charges, visibility, and more.

Understanding structuralModel Attributes

structuralModel attributes belong to the sm attribute space and apply specifically to structural model nodes in SAMSON. Each attribute has a short name for simple queries and supports a variety of value types, including integers, booleans, and floats.

Key Attributes for Your Workflow

  • numberOfAtoms (sm.nat): Filter models based on the number of atoms. For instance:
    • sm.nat > 100: Matches models with more than 100 atoms.
    • sm.nat 100:200: Matches models with atom counts between 100 and 200.
  • numberOfChains (sm.nc): Identify models with a specific number of chains. Examples:
    • sm.nc < 3: Matches models with fewer than 3 chains.
    • sm.nc 2:4: Matches models with 2 to 4 chains.
  • formalCharge (sm.fc): Filter by total formal charge. Examples include:
    • sm.fc 1: Matches models with a formal charge of 1.
    • sm.fc 6:8: Matches models with charges between 6 and 8.

How It Saves You Time

These attributes can significantly reduce the effort needed to pinpoint nodes with desired characteristics. For example, when working on a protein with a specific number of chains or residues, rather than manually searching through all nodes, you can use sm.nc or sm.nr to instantly isolate relevant models. Similarly, if you’re analyzing the electronic properties of a molecule, the formalCharge attribute provides a quick way to filter structures of interest.

Extended Filtering Options

The structuralModel attribute space offers additional capabilities, such as:

  • Ownership-related attributes: For example, ownsMaterial (sm.om).
  • Boolean attributes: Attributes like visible (sm.v) and hidden (sm.h) allow you to manage visibility at a granular level.
  • Detailed atomic counts: Attributes like numberOfOxygens (sm.nO), numberOfCarbons (sm.nC), and numberOfHydrogens (sm.nH) make it easier to refine structures based on composition.

Wrapping Up

Whether you’re managing a large number of structural models or conducting targeted analyses, the structuralModel attributes in SAMSON enable you to focus on what’s most relevant. With attributes for everything from atom counts to charges, this feature caters to a wide variety of molecular modeling needs.

Discover the full list of attributes and further examples in the official SAMSON documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.

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