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A simple technique for visualizing atomic trajectories in your animation presentations

Have you ever needed to visualize how atoms move over time during your molecular animation? Whether you’re showcasing a docking process, simulating molecular dynamics, or illustrating a mechanism of action, a common challenge is to record and later export clear…

Refining Protein Backbone Conformations Using Dihedral Angle Editing

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Validating and refining protein structures often involves ensuring that backbone conformations fall within energetically favorable regions. When dihedral angles (φ and ψ) are off, a residue may adopt a strained conformation that can compromise structural stability or the results of…

Which Symmetry Group Should You Trust When Modeling Large Assemblies?

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When working with large biological assemblies—such as viral capsids, multimeric protein complexes, or nanostructures—symmetry can be both a friend and a challenge. Detecting symmetry reduces computational load and helps identify biologically meaningful patterns. But what happens when multiple symmetry groups…

Stop guessing: how to filter notes by visibility, name, and more in SAMSON

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When managing complex molecular models in SAMSON, clarity is key. If you’ve ever struggled with too many annotations cluttering your workspace—especially when trying to track down specific notes—this post is for you. In SAMSON, “note” nodes are useful for organizing…

Avoid Losing Measurements When Modeling Molecules

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As a molecular modeler, it’s common to examine distances, angles, or torsions between atoms—but it’s equally common to lose track of those measurements when switching views or making a new selection. If you’ve ever thought, “Where did my previous distance…

Can’t open your molecular file? Here’s what to do

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Molecular modelers often encounter a familiar frustration: you download a dataset from a database, receive a file from a collaborator, or export something new from your lab’s instrument software… only to find that your modeling platform can’t open the file.…

Easily Find Atoms, Residues, and More with NSL in the Document View

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Molecular modelers often work with complex structures containing thousands of atoms, residues, ligands, and other node types. Selecting the right subset of these nodes precisely and efficiently can be a challenge, especially during structure analysis, preparing simulations, or performing molecular…

Using Your Own GROMACS Installation in SAMSON: Why and How

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Many molecular modelers rely on GROMACS to simulate molecular dynamics because of its flexibility, performance, and open-source nature. While integrative platforms like SAMSON offer out-of-the-box integration with GROMACS, a common need arises: what if your project requires a specific version…

Quickly Find Segments with Specific Molecular Properties in SAMSON

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When designing or analyzing biological macromolecules, one of the most time-consuming tasks is filtering or locating specific parts of your molecular model. For example, you might need to: Find all protein segments with more than 100 residues Identify RNA segments…

A Simpler Way to Show Molecular Disassembly

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When presenting complex molecular mechanisms or structural transitions, molecular modelers often encounter a recurring problem: how to clearly communicate spatial changes without overwhelming their audience. Whether your goal is to demonstrate a protein’s binding interface or visually highlight subunit relationships,…