SAMSON Blog – Page 314

Avoiding Costly Mistakes with the History Feature in SAMSON

It’s happened to every molecular modeler: hours spent refining a complex structure, carefully adjusting geometry or interaction parameters, only to lose a crucial state after a slip of the mouse or an unexpected action. For those using SAMSON, the integrative…

Bring Your Own Code: Integrate External Tools into SAMSON Easily

OneAngstrom

Many researchers and developers in molecular modeling rely on custom scripts, external executables, or web services to perform specific tasks—such as docking, calculations, or data analysis. However, managing multiple tools can be time-consuming, especially when interoperability isn’t seamless. This is…

Quickly Select and Show Only What Matters in Your Molecular Scene

OneAngstrom

When your molecular scene becomes crowded with visual models, it’s easy to lose focus. Whether you’re preparing images for publication, analyzing a specific interaction site, or debugging a custom SAMSON app, you likely spend time toggling visibility and manually sifting…

How to Quickly Target File Nodes in SAMSON with NSL Filters

OneAngstrom

Managing large molecular projects in SAMSON? If you’ve ever found your workspace filled with dozens of files, and struggled to apply filters or actions only to specific file nodes (and not the nodes inside them), you’re not alone. This is…

Make Molecules Fade, Not Teleport — Disappearing Objects in SAMSON

OneAngstrom

If you’ve ever built an animation of a molecular system and felt frustrated by the sudden disappearance of elements—like they just vanish from the scene without context—you’re not alone. Molecular modelers often need to visually transition elements out of view…

Tired of Repeating Molecular Simulations? Use Batch Projects in SAMSON

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If you’ve ever run molecular dynamics simulations for multiple conformations of the same molecule, you know how tedious it can be to repeat the same setup steps over and over. Whether you’re iterating through a ligand binding pathway or comparing…

Paths vs. Conformations: Which to Use with the P-NEB Method in SAMSON?

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When modeling molecular transitions such as ligand unbinding or conformational changes in biomolecules, predicting realistic pathways is often critical, but far from straightforward. Finding the most efficient and accurate approach can save time and computing resources, especially when working with…

Removing Unwanted Chains Before Molecular Interpolation: A Quick Tutorial

OneAngstrom

When working with protein structures, accuracy begins at preparation. One common issue molecular modelers face—especially when dealing with alternate conformations or large multimeric structures—is the need to remove unwanted chains before running simulations, conformational interpolation, or structural comparisons. For instance,…

Saving and Exporting Protein Conformations Without Losing Valuable Motion Data

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Capturing molecular flexibility is an essential part of modern structural biology and computational modeling. Whether you’re exploring ligand accessibility, visualizing allosteric motions, or preparing morphing animations between conformations, there often comes a time when you reach an interesting molecular state…

Faster Molecular Geometry Optimization with FIRE in SAMSON

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When building or analyzing molecular structures, geometry optimization is essential to remove unrealistic geometries and prepare systems for simulations. However, classic approaches such as steepest descent can be time-consuming, especially when your structure requires large-scale structural relaxation. Fortunately, SAMSON offers…