OneAngstrom – Page 272

Molecular Modeling Isn’t Easy—But SAMSON’s Interactive Tutorials Make It Simpler

For many molecular modelers, the early stages of using a new software platform can feel like learning a foreign language. From navigating a complex interface to figuring out how to run simulations or analyze data, the learning curve can be…

Working with Molecular Dynamics Trajectories in SAMSON

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Molecular modeling and simulation often involve handling large trajectory files produced by molecular dynamics engines like GROMACS, AMBER, NAMD, LAMMPS, and Tinker. However, switching between simulation and visualization tools can feel like constantly battling with incompatible data formats and slow…

Avoiding Costly Mistakes with the History Feature in SAMSON

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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

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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

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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

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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

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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

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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,…