Author: OneAngstrom

Creating effective scientific animations often comes down to highlighting just the right parts of a molecular system at the right moment. If you’re preparing a presentation or a video to communicate your latest discovery, you probably don’t want all atoms…

As a molecular modeler working with DNA nanostructures, it’s common to design sophisticated geometries digitally, only to find yourself wondering how these can be simulated effectively. Bridging the gap between interactive design and coarse-grained simulation is essential — and this…

When starting out with molecular modeling in SAMSON, one of the first challenges you may encounter is how to make your molecular structures both informative and visually clear. Whether you’re preparing a figure for a publication or trying to make…

When simulating molecular systems, it’s common to analyze dynamic regions that are central to your research – such as active sites, interface regions, or specific complexes. But as the system evolves over time, how can you always keep your eyes…

When preparing a biomolecular system for simulation with GROMACS, removing existing crystal waters is often part of the workflow. But not all water molecules are equal—some are tightly bound and participate directly in biochemical function, especially near active sites. Removing…

When building compelling molecular presentations or demonstrating mechanisms in your chemical or biological models, static visuals often fall short in conveying dynamic behavior. Were you ever in a situation where highlighting part of your model felt like not enough—where you…

One of the frequent challenges in molecular modeling is effectively communicating 3D structures and interactions to colleagues, students, or collaborators. Screenshots and static views are often not enough, especially when trying to showcase binding pockets, active sites, or conformational changes.…

Long sessions of molecular modeling can be visually demanding, especially when working with bright user interfaces in low-light environments. If you’re using SAMSON, the integrative platform for molecular design, there’s a simple way to reduce eye fatigue: switching to Dark…

When visualizing complex molecular systems, clarity is essential. Often, parts of a structure temporarily obstruct your view of regions of interest, such as an active site or a particular interaction interface. While hiding parts of the model solves this problem,…