Author: OneAngstrom

Molecular modeling often involves watching how a ligand binds to or unbinds from a protein. But extracting only relevant atomic coordinates for simulations like free energy calculations can be tedious — especially if your tool exports everything indiscriminately. What if…

When performing molecular mechanics simulations, using force fields like the Universal Force Field (UFF) is a standard and powerful approach. However, researchers often find themselves frustrated when their simulations don’t quite behave as expected—energy plateaus, unrealistic geometries, or convergence issues.…

For many molecular modelers, generating 2D diagrams of protein-ligand interactions is a foundational yet repetitive task. These diagrams are essential to illustrate key interatomic contacts, but customizing them to make them readable and publication-ready can feel like an endless layout…

Creating photorealistic molecular visuals can be time-consuming if each element needs to be manually styled. Whether you’re working on a publication figure, a presentation, or simply want to explore your models with more visual clarity, adjusting visual materials quickly and…

When working on molecular modeling projects, precise positioning of atoms, fragments, and molecular assemblies isn’t just helpful—it’s critical. Whether you’re preparing a simulation, visualizing structures, or creating educational animations, having solid control over how you manipulate objects in 3D space…

When modeling molecular systems, predicting how a molecule transitions from one conformation to another—especially through complex pathways like ligand unbinding—is a frequent challenge. While generating an initial path using interpolation or sampling is a good start, these paths are rarely…

Molecular modelers often need to closely inspect the transitions and conformational changes in molecular systems. While forward animations help reveal how a molecule evolves over time, there is often as much insight to be gained by watching it happen in…

Molecular modelers often face the challenge of visual clutter when presenting large or intricate systems. Whether you’re creating visualizations for publications, tutorials, or presentations, overlapping atoms or structures can obscure the message you’re trying to convey. A critical—and often overlooked—solution…

When you’re modeling large molecular systems—dense proteins, layered assemblies, or binding site environments—it’s easy to feel like you’re navigating a fog. Important details get buried under overlapping atoms, useful parts are occluded, and your camera feels like it’s fighting against…