OneAngstrom – Page 81

From Conformations to Transition Paths: A Practical Guide to the NEB Method in SAMSON

Predicting how molecules transition from one state to another is at the heart of molecular modeling. Whether you’re studying protein folding, ligand binding, or conformational changes, knowing the minimum energy path (MEP) between two states can shed light on kinetics…

From Zero to Simulating: Installing SAMSON Without Admin Rights

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If you’ve ever tried installing scientific software in a university or institutional setting, you’ve likely run into a familiar obstacle: you don’t have admin rights. Maybe you’re working on shared lab computers, maybe IT is hard to reach, or maybe…

Quickly Identify Charged Regions in Molecular Models Using Structural Group Attributes

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When analyzing complex molecular systems, it’s common to face the challenge of identifying specific regions based on electrostatic properties. For instance, you may want to quickly locate highly charged structural groups that could be involved in salt bridges, ionic interactions,…

What Makes SAMSON Editors So Useful for Molecular Modeling Tasks?

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Anyone working in molecular modeling knows that navigating structural complexity is part of daily life. Whether building a model from scratch or modifying existing biomolecules, the ability to interactively edit molecular systems in a flexible, precise manner can dramatically reduce…

From SMILES to 3D Structures in Seconds with SAMSON

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For many molecular modelers and cheminformatics researchers, going from a simple SMILES string to a complete 3D structure can involve cobbling together multiple tools, scripts, or web platforms. This can be time-consuming and disrupt workflow—especially when working with large datasets.…

Drawing Carbon Nanotubes by Hand: Quick Interactive Modeling in SAMSON

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Building carbon nanotube (CNT) models is often a central need in molecular modeling, nanoscience, and materials simulation. Whether you’re designing CNT-based sensors, creating nanostructures for simulations, or exploring their mechanical and electronic behavior, the ability to quickly and intuitively generate…

Speed Up Protein Structure Predictions with AlphaFold-2 in SAMSON

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Predicting accurate protein structures remains one of the most time-consuming steps in molecular modeling and drug discovery. Researchers often struggle with limited local hardware, complex pipelines, and long waiting times using public services. Fortunately, SAMSON offers an integrated and user-friendly…

Prevent Unwanted Camera Movements in Molecular Animations

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If you’ve ever created a molecular animation and noticed that the camera angle changes unexpectedly between frames — even though you didn’t mean to animate it — you’re not alone. This can be frustrating, especially when you want a specific…

Never Lose Sight of Key Molecules During Simulations

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When running molecular dynamics or simulating binding events, one common frustration lies in losing track of what’s most important—the atoms or regions you’re examining. Camera movements can end up drifting, making it difficult to stay focused on key interactions or…

Choosing the Right Symmetry Group in Large Molecular Assemblies

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When modeling large protein complexes, viral capsids, or other biological assemblies, symmetry can be both a powerful ally and a source of confusion. One challenge commonly faced by molecular modelers is deciding which symmetry group to retain when a structure…