When modeling biomolecular systems, it’s common to compute pathways for ligand binding or unbinding. Whether you’re performing free energy profiling, setting up enhanced sampling simulations, or simply visualizing molecular movement, you often only need the atomic coordinates of a ligand—not…

When visualizing molecular models, color is more than aesthetic—it’s a communication tool. Whether you’re highlighting atom types, representing molecular groups, or differentiating between molecular chains, selecting the right color palette helps make your models intuitive and easier to interpret. But…

Visualizing molecular measurements—like distances, angles, or torsions—plays a vital role when modeling or analyzing molecular structures. Often, you’re examining multiple interactions simultaneously, especially when comparing conformers or tracking structural changes during simulations. But how do you avoid clutter while maintaining…

When presenting molecular models to an audience—whether it’s in a classroom, during a group meeting, or at a conference—how atoms and structures appear can have a surprisingly big impact on clarity. Abrupt visual transitions are jarring, and make it harder…

Setting up a molecular dynamics simulation that involves a reaction coordinate—such as a ligand unbinding pathway—can be time-consuming. One frequently reported pain by molecular modelers is the extraction of atomic coordinates along a pre-defined path for use in free energy…

Staring at bright screens for hours can be exhausting — especially for molecular modelers who often spend long sessions analyzing complex structures. Whether you’re building interaction models, rendering simulations, or working late into the night, eye fatigue is a common…

When creating molecular animations for presentations or publications, molecular modelers often face the challenge of showing molecular structures gradually vanish—without making it look abrupt or confusing for the audience. While the classic ‘Hide’ effect can switch off visibility instantly, sometimes…