SAMSON Blog – Page 72

A Simple Way to Query File Nodes in Your Molecular Models

When working with complex molecular systems in SAMSON, it’s common to handle multiple datasets, simulations, or structural variations, each encapsulated in distinct file nodes. Whether you’re juggling docking runs or importing external molecular files, a recurring need arises: how do…

Defining Custom Monomers for Smarter Polymer Design

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Designing complex polymers with specific properties often starts with the simplest building block: the monomer. But if you’ve ever needed to go beyond standard monomer libraries to define your own, you know how tedious that process can be in many…

Easily Select Negatively Charged Residues (And Other Filters) in SAMSON with NSL

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When working with macromolecular structures, a common challenge for molecular modelers is to efficiently identify and manipulate residues that meet specific biochemical or structural criteria. Whether you’re preparing a protein for simulation, adjusting protonation states, or studying interactions near active…

When Structures Let Go: Introducing the Undock Animation in SAMSON

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In molecular modeling, visual storytelling plays a surprisingly important role. Whether you’re preparing a scientific talk, teaching structural biology, or simply trying to understand how two molecules interact—or stop interacting—animation can provide clarity that static images often can’t. One common…

When Zooming Isn’t Enough: Using Dolly Camera Animation in SAMSON

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When working on molecular systems, being able to clearly communicate what you are seeing is just as important as understanding what you are looking at. Capturing smooth transitions for presentations, tutorials, or publications can be a challenge, especially when you…

Quickly Switch Between Molecular Selections with Quick Groups in SAMSON

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When working on complex molecular systems — such as proteins with multiple ligands, solvated complexes, or multimeric structures — it’s common to revisit specific components repeatedly. Selecting a ligand, then moving to a receptor, and later examining water molecules or…

Making Molecular Models More Engaging with Subtle Rocking Motions

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One common challenge in molecular modeling and visualization is keeping audiences visually engaged during presentations—especially when presenting static structures. While it’s easy to become absorbed in your own structural analysis, collaborators or students may struggle to connect with the material…

Avoiding Common Pitfalls in NPT Equilibration with GROMACS Wizard

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One of the most delicate steps in molecular simulation workflows is the NPT (isothermal-isobaric) equilibration phase. After energy minimization and temperature stabilization via NVT equilibration, the next goal is to ensure that your system reaches a stable density under the…

Unhiding Insights: Mastering Node Visibility in SAMSON

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Molecular modeling projects often become complex quickly, especially when managing large biomolecules with multiple layers of information. One common source of inefficiency is trying to locate or interact with nodes that are unexpectedly invisible. Whether it’s visualizing a hidden ligand…

Understanding Visual Models in SAMSON: More Than Just Looks

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For many molecular modelers, clarity in visualization is more than aesthetic—it’s essential for understanding structure, function, and interaction. Whether you’re interpreting protein folding or preparing visual outputs for a publication, good molecular graphics save time and reduce risk of misinterpretation.…