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…

When exploring protein function or designing ligands, it’s often essential to compare specific functional regions, rather than entire protein structures. This is especially true in structure-based drug discovery, homology modeling, and evolutionary studies, where conserved motifs might be hidden among…