Understanding Chain Attributes for Molecular Modeling in SAMSON

Molecular modelers are often tasked with specifying and analyzing complex molecular systems. One of the significant challenges is filtering and identifying specific components in these systems. For instance, molecular chains often consist of numerous atoms, residues, and structural groups. Handling this complexity can be daunting without a structured method to organize and query the relevant data. This is where SAMSON’s Chain Attributes come into play.

The Chain Attribute Space in SAMSON, referred to as c, allows modelers to define and target specific attributes of molecular chains. These attributes streamline the process of working with chain-level data and enable precise selection and filtering of chain components. Let’s dive into some essential chain attributes and practical ways to make use of them.

Inherited vs. Specific Attributes

Chain attributes are classified based on their origin: inherited from node or structuralGroup attribute spaces, and specific to the chain attribute space.

For instance, inherited attributes from the node attribute space include:

  • hasMaterial (hm): Specifies whether the chain has material. Values: true/false. Example: c.hm or not c.hm.
  • hidden (h): Marks whether the chain is hidden. Values: true/false. Example: c.h or not c.h.
  • selected: Checks if the chain is currently selected. Example: c.selected or not c.selected.

From the structuralGroup attribute space, you inherit practical attributes like:

  • numberOfAtoms (nat): Defines the total number of atoms in a chain. Example: c.nat < 1000 or c.nat 100:200.
  • numberOfCarbons (nC): Focuses on the number of carbon atoms in the chain. Example: c.nC < 10 or c.nC 10:20.
  • partialCharge (pc): Represents floating-point values for the chain’s partial charge. Example: c.pc > 1.5.

Specific to chain attributes, we have:

  • chainID (id): Matches chains with specific IDs. Example: c.id 1 or c.id 2:4,6. This is particularly useful when modeling systems with multiple chains.
  • numberOfResidues (nr): Filters chains by the number of residues. Example: c.nr > 130 or c.nr 100:130.
  • numberOfSegments (ns): Targets chains with specific numbers of segments. Example: c.ns < 3 or c.ns 1:3.

Practical Examples

The real value of these attributes becomes clear in day-to-day modeling tasks:

  • Focus solely on visible chains: c.v.
  • Select chains with more than 200 atoms but fewer than 10 carbons: c.nat > 200 and c.nC < 10.
  • Isolate chains with chain IDs in a specific range: c.id 1:5.
  • Examine chains with a formal charge greater than 1.5: c.pc > 1.5.

How Can This Help You?

By leveraging chain attributes, molecular modelers can reduce complexity, save time, and enhance their workflows. For example, filtering out irrelevant chains in a large protein complex becomes simple and efficient. This functionality ensures that you focus on the most relevant data for your analysis or design tasks.

Not only does this make your work faster, but it also reduces human error when interacting with complex molecular models. For anyone working with molecular systems in SAMSON, mastering chain attributes is a must.

To see the full list of chain attributes and learn more, visit the official documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at SAMSON Connect.

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