Author: OneAngstrom

Have you ever wrestled with clarity while recording molecular animations? Whether you’re creating a presentation for a research talk or designing educational material, sometimes the challenge is simply: how do I make parts of a molecular structure disappear at the…

When working on complex molecular modeling projects, it’s easy to feel overwhelmed by the growing number of molecular structures, edits, and simulation elements. Proteins, ligands, solvents, surfaces, cameras, animations—everything piles up, and soon you’re asking: where did I put this…

When preparing molecular animations, one of the most common frustrations is discovering that your camera angle — the precise view you’ve carefully adjusted — has unexpectedly shifted later in the animation. This often happens because while you’re editing molecular motions,…

For many scientists working on molecular modeling, the first hurdle is often the software itself. Despite being powerful, complex modeling environments like SAMSON can feel overwhelming for newcomers. What should you click? Where are the tools? How do you actually…

Molecular modelers often rely on multiple specialized tools during structure preparation, simulation setup, or analysis stages. If you’re using SAMSON, you’ve probably noticed that the platform includes a feature-rich environment where ‘editors’ allow direct manipulation of molecular models in the…

When setting up molecular dynamics simulations, a common obstacle for many molecular modelers is ensuring that simulation inputs are correct and properly referenced. This becomes particularly crucial during the equilibration phase, where one wrong file can cost time and resources.…

When constructing molecular systems, a frequent challenge faced by researchers is correctly orienting molecular fragments before and after placement. Improper orientations can lead to overlapping atoms, energetically unfavorable structures, and ultimately incorrect simulation results downstream. SAMSON provides several integrated tools…

When working with molecular modeling, force fields like the Universal Force Field (UFF) can automatically determine atom types, bonds, and bond orders based on molecular geometry. While this is convenient, it can sometimes lead to frustrating mismatches if the automatic…

One common challenge in molecular modeling is distinguishing molecular features in dense or complex structures. When visualizing intricate biomolecular environments, depth perception becomes crucial to avoid misinterpretation — especially when analyzing binding interfaces, cavities, or packed atom regions. That’s where…

One of the challenges molecular modelers often face is the lack of real-time feedback when manipulating structures. Whether you’re refining a structure, adjusting a geometry, or exploring potential distortions, waiting for a full simulation step—or hitting “run” dozens of times—can…