OneAngstrom – Page 24

Quickly Select Chains by Properties in SAMSON Using the NSL

Working with molecular models that include multiple chains can often feel overwhelming—especially if you’re trying to select or isolate specific chains based on unique criteria. Whether you’re preparing a simulation, analyzing a structure, or simply cleaning up a model, being…

Tracing Molecular Motion with Center-of-Mass Pathlines

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One of the common challenges for molecular modelers is understanding how molecular components move during simulations. Whether you’re tracking a ligand unbinding from its binding pocket or studying large conformational transitions in proteins, getting a clear view of motion across…

Why Your Molecules Don’t Break Apart When You Move Atoms in SAMSON

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When building or editing molecular systems, small tweaks often lead to unexpected results. Move an atom, and you might accidentally break a bond. Shift a structure, and suddenly your topology is no longer valid. This is especially painful when iteratively…

How to Efficiently Target Node Groups in SAMSON Using Attributes

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If you’ve worked with complex molecular models in SAMSON, you know the importance of managing selections precisely. Whether you’re applying simulations or merely reorganizing your design, selecting the right node groups—without affecting too many unrelated parts—can be key to your…

How to Preview and Generate Symmetry Mates in SAMSON Without Breaking Your Workflow

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If you work with protein structures from the Protein Data Bank (PDB), you’ve likely encountered files that only include the asymmetric unit of a biological assembly. While useful, that limited view hides the full structural context proteins adopt in crystals…

When Everything is a Node: Understanding Molecular Model Structures in SAMSON

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One of the challenges often faced by molecular modelers — whether they’re working in drug discovery, materials science, or structural biology — is managing the complexity of molecular data. In a large molecular system, how do you make sense of…

Making Molecules Appear at the Right Time in Your Animations

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When preparing molecular animations, timing is everything. If you’re showing a protein interaction, reaction mechanism, or structural transition, you often want specific molecules or components to become visible at just the right moment. Many molecular modelers struggle with objects either…

Controlling Pocket Motions with Nonlinear Normal Modes in SAMSON

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One of the recurring challenges in computational structural biology is understanding and predicting how biomolecules open or close around functional sites, such as ligand-binding pockets. Experimental structures often show only a few static snapshots—yet the biological activity is tightly linked…

How to Filter Specific Bond Types in Your Molecular Models

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Identifying and working with specific bond types can be a routine but time-consuming task for molecular modelers. Whether you’re validating a structure, preparing a molecule for simulation, or analyzing chemical behavior, being able to quickly select bonds like single, double,…

How to Select Chains by Atom Count, Element Types, or Charge in SAMSON

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If you’ve ever needed to filter biomolecular chains based on atom count or elemental composition, you’re not alone. Molecular modelers often need to isolate chains with specific structural properties — such as chains with fewer than 500 atoms, or chains…