Author: OneAngstrom

When working with molecular simulations or modeling, one of the most common visualization challenges involves communicating structural dynamics effectively. There are times when entire groups of atoms, residues, or molecules should fade in and out of view to direct attention,…

When you’re trying to build a clear and engaging molecular animation, timing is everything. Whether preparing a conference presentation, an educational video, or just showing an interaction mechanism to colleagues, how and when a molecule appears on screen can significantly…

In polymer design, starting with the right building blocks can make all the difference. If you’re creating custom polymers in SAMSON, one of the first steps is often registering monomers—your fundamental repeat units. But many modelers don’t realize just how…

One of the recurring challenges in molecular modeling is presenting molecular dynamics in a compelling and intuitive way. If you’ve ever tried to create a smooth animation of a ligand moving through a binding pocket or a protein folding over…

One of the recurring challenges faced by molecular modelers is identifying and triggering functionally relevant conformational changes in biomolecules—such as the opening of a binding pocket—without resorting to computationally intensive simulations. Normal mode analysis (NMA) offers a far more efficient…

Molecular modelers working with large structural datasets often face the challenge of visually demonstrating how different biomolecules interact. Whether you’re presenting receptor-ligand binding events, assembling complex biomolecular systems, or simply trying to communicate structural hypotheses, an animation can go a…

When building, comparing, or preparing molecular models for visualization or simulation, one common issue faced by modelers is the orientation and relative positioning of molecular structures. Misaligned molecules can complicate analysis, generate cluttered views, and obstruct accurate measurements or transformations.…

Understanding how your ligand interacts with a receptor at the atomic level is key to rational drug design. However, many molecular modelers spend a surprising amount of time just trying to generate clear, informative visuals of binding sites. If you’re…

When visualizing complex molecular systems, spatial perception plays a crucial role. You need to know what atom is behind or in front, how close molecular structures are to each other, and how everything fits together in 3D space. But sometimes,…