OneAngstrom – Page 170

Quickly Identifying Files of Interest in Molecular Projects

As molecular modeling projects grow, so does the number of files within them. If you’ve ever found yourself scrolling endlessly through a complex data tree in SAMSON just to locate the right file, you’re not alone. Fortunately, the Node Specification…

Why Your Molecular Animation Suddenly Jumps—And How to Fix It

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Molecular visualizations can be powerful storytelling tools. Whether you’re preparing a presentation, a scientific movie, or just documenting your molecular model’s behavior over time, a smooth camera trajectory is crucial. However, many molecular modelers have encountered this frustrating issue: suddenly,…

Keeping Your Molecules in Focus: Tracking with a Fixed Camera

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When visualizing molecular dynamics, staying focused—literally—can be a challenge. Molecules twist, bend, and tumble through space, and it’s easy to lose track of specific atoms or active regions as they shift across the screen. But what if your camera could…

When Bonds Break (and Form): Interactive Topology in Molecular Modeling

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Modeling molecular systems doesn’t always go smoothly. Sometimes, atoms need to connect. Other times, bonds have to break. In those moments, traditional molecular force fields—designed for static topologies—can get in the way. You might find yourself re-typing your molecules, manually…

Installing SAMSON Without Admin Rights: What You Need to Know

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If you’ve ever had to install complex software in a shared or tightly managed computing environment, you’ve likely run into a common problem: needing administrator rights. For many molecular modelers—especially students, researchers in government labs, or users of institution-managed systems—this…

Choosing Initial Conformations for Umbrella Sampling in SAMSON

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One of the common challenges in setting up Umbrella Sampling simulations is selecting the right initial conformations. For many molecular modelers, this step requires scripting, plotting distances manually, or running external tools—often a time-consuming process. Fortunately, SAMSON’s GROMACS Wizard streamlines…

Easily Reposition Views in Molecular Animations Using Keyframes

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Creating smooth and informative molecular animations often means guiding your audience’s eyes exactly where you want them to look. Whether you’re rotating around a binding site or zooming through a channel, camera movement is critical. However, many molecular modelers find…

Quickly Find and Control Labels in Molecular Models

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When working with complex molecular models, labeling atoms, groups, or other elements is often essential to communicate ideas, track changes, or set up simulations. However, once those labels start to accumulate in a scene, managing them can become difficult: Which…

Identify Molecular Models with Specific Atom Counts: A Practical Guide for Structural Filtering

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When working with large molecular systems, selecting or filtering models based on specific structural criteria can be extremely useful. Whether you need to analyze models with fewer than 100 atoms for performance reasons, or zoom in on structures with a…

Not Just a Movie: Capturing Atom Trajectories with the Record Path Animation in SAMSON

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When working with molecular models, visualizing motion is not only helpful—it’s often essential. Whether you’re simulating a docking process, building a molecular assembly, or simply illustrating atomic movements for a presentation, being able to capture trajectories of atoms over time…