In molecular modeling, it’s not uncommon to end up with large amounts of trajectory data—often more than you need. Perhaps you’re studying just a ligand’s movement through a protein tunnel, or only the backbone motion during a conformational change. Exporting…

One of the common challenges in setting up umbrella sampling simulations is preparing a good set of initial conformations. Molecular modelers often struggle to extract regular conformations from trajectories or paths, identify reaction coordinates properly, and automate the setup process…

Molecular visualizations communicate complex structural information. But if you’ve ever found your protein coloring scheme hard to interpret—or worse, misleading—you’re not alone. Poor color choice can obscure relevant features, strain the eyes, or confuse colleagues with color vision deficiencies. Fortunately,…

One common challenge faced by molecular modelers and scientific illustrators is creating images that are not only scientifically accurate, but also visually compelling. For presentations, publications, or science communication, the visual quality of molecular graphics plays a crucial role in…

Sometimes, the latest version of a software tool just doesn’t meet all your current needs. Maybe you’re collaborating with a colleague who uses an earlier release, or perhaps a key extension you rely on hasn’t yet been updated to support…

Designing and simulating DNA origami structures has become an increasingly important part of molecular modeling and nanotechnology research. Whether you’re designing nanorobots, cages for drug delivery, or programmable matter, one common frustration is the challenge of managing and visualizing complex…

Choosing how to visually represent molecular structures is more important than it might first seem. Often, clarity and insight depend as much on color selection as on structure accuracy. When you’re comparing molecular parts, highlighting specific regions, or distinguishing components…

When working with complex molecular systems, it’s often important to isolate specific atom groups for visualization or modification. Yet, selecting atoms manually can become tedious and error-prone, especially with large systems like crystals, biomolecules, or nanostructures. SAMSON’s Atoms Selector Extension…

Molecular modelers often need to visualize how molecules or fragments dissociate after docking — for instance, to show unbinding pathways, ligand release mechanisms, or just reverse a previous docking animation. Doing this manually, while attempting to create smooth, understandable animations,…