OneAngstrom – Page 12

More Than Just Zoom: Using the Dolly Camera to Spotlight Molecular Details

Have you ever created a molecular animation, only to feel like it didn’t quite bring the attention exactly where you intended? Maybe you tried using a simple zoom, and while the camera got closer, the movement lacked fluidity or precision…

When Atoms Appear: Visualizing Molecular Assembly with Reveal Atoms

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Communicating complex molecular processes often requires showing how a molecule forms or changes over time. But static images — or even basic animations — can fall short when you’re trying to illustrate a structural assembly or interaction step-by-step. One of…

Making Molecules Breathe: A Visual Trick to Enhance Structural Transitions

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Clarity and visual communication are major challenges in molecular modeling. When crafting animations to illustrate complex molecular phenomena—such as binding events, structural adjustments, or phase transitions—it’s common to feel limited by basic visualization tools. Animations can quickly become cluttered or…

Avoiding Clashes When Solvating Coarse-Grained Systems in GROMACS

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Working with coarse-grained (CG) models is a common strategy for simulating larger molecular systems with reduced computational cost. However, when preparing these systems for molecular dynamics (MD) simulations, one subtle but critical issue often trips up even experienced modelers: the…

Making Molecular Objects Disappear (and Reappear) with Precision

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In molecular modeling, clear communication is essential. Whether you’re presenting a mechanism to collaborators or preparing a visual for publication, controlling the visibility of molecules or molecular fragments at specific times can dramatically improve audience understanding. This is where the…

Creating Custom Molecular Interactions in SAMSON Without Coding

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Being able to define and manipulate molecular interactions is essential when designing or analyzing molecular systems. From modeling hydrogen bonds to setting up protein–ligand docking environments, molecular modelers frequently need to go beyond visualization and directly interact with the system.…

Making Molecular Models Move: How to Use the Undock Animation in SAMSON

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When preparing a molecular animation or visualizing a docking scenario, one common challenge modelers face is illustrating the actual undocking process of ligands, proteins, or other structural components. Creating this visualization manually could take a significant amount of time and…

Filtering Molecular Structures by Atom Counts in SAMSON

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If you’ve ever worked with large molecular datasets, you know how valuable it is to filter and select structures based on their composition. Whether you’re modeling organic molecules, studying reaction mechanisms, or analyzing biomolecular systems, identifying specific groups based on…

Dragging Atoms, Watching Molecules Respond: A Closer Look at Interactive Simulation in SAMSON

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Simulating molecular movement is a core task for many researchers, but getting immediate feedback from changes made in a visual editor is often time-consuming or unavailable altogether in some tools. One common pain point in molecular modeling is not being…

Visualizing Atomic Defects in Diamond Structures with SAMSON

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Crystals may seem perfect in textbooks, but in the real world, they’re far from flawless. Atomic defects—tiny irregularities in the structure—can have dramatic effects on material properties like conductivity, strength, and color. For molecular modelers and materials scientists, simulating and…