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Three Lesser-Known Ways to Tune UFF Simulations in SAMSON

If you’ve worked with molecular simulations using the Universal Force Field (UFF), you’ve probably faced this common struggle: finding the right parameters to reflect the behavior of your specific system. Accurate simulation results often require tweaking below the surface—beyond simply…

What Are SAMSON Apps, and Why Should Molecular Modelers Care?

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For molecular modelers, one of the biggest challenges is bridging the gap between different computational tools, data formats, and specific modeling functionalities. Whether you’re preparing structures, performing simulations, or visualizing molecular systems, you may find yourself juggling many different software…

Filtering Molecular Models by Partial Charge for Cleaner Simulations

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When preparing molecular systems for simulation or analysis, one often faces large sets of structural models from databases or previous computational experiments. These models may vary widely in their structural, chemical, and electrostatic properties. One important attribute that scientists often…

A Precise Way to Select Atoms with Mathematical Expressions

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When working with molecular structures, atom selection can become a tedious and repetitive task, especially in large systems like crystals, biomolecules, or complex nanostructures. Often, modelers want to focus on specific regions — say, atoms with certain charges, atoms within…

Want to Add Your Own Molecular Modeling Tools? Here’s How to Create a SAMSON Extension

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Molecular modelers often have a favorite script, algorithm, or visualization routine they reach for—something they’ve fine-tuned to match their workflow. But integrating these custom tools into large, extensible platforms can feel out of reach without advanced programming setups, complicated builds,…

Quickly Select Atoms with Math: A Better Way to Tame Big Structures

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When working with large molecular assemblies, crystal structures, or intricate protein systems, selecting the right atoms can be surprisingly time-consuming. Graphical selection tools may work well for small molecules, but they tend to get messy when you’re dealing with thousands—or…

Less Eye Strain, Better Focus: Using Dark Mode in SAMSON

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If you’re spending long hours working on molecular models, you’ve probably noticed how harsh bright interfaces can be on the eyes—especially in low-light environments. Whether you’re modeling late into the night or simply prefer a more subdued interface, SAMSON’s dark…

Quickly Filtering Backbone Groups in Complex Molecules

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When designing, analyzing, or editing macromolecular systems in SAMSON, researchers often need to isolate specific backbone groups based on their chemical or visual characteristics. Whether it’s identifying hidden segments of a protein, locating backbones with extremely high partial charges, or…

Make Molecules Appear at the Right Time: Using the Show Animation in SAMSON

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Creating compelling molecular presentations isn’t just about pretty graphics — it’s about telling a story. Molecular modelers often struggle with managing the visibility of atoms, molecules or entire structures over time, especially during animated timelines where some structures need to…

Skip the Menus: Using Natural Language to Command SAMSON AI

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For molecular modelers, repetitive tasks like removing solvent molecules, generating molecular surfaces, or adjusting visual styles are a constant part of the workflow. Traditionally, these actions require navigating through multiple menus in a complex interface. Over time, this can be…