When presenting a molecular scene, one common challenge is building a focused yet smooth transition between frames—especially when you’re trying to guide the viewer’s attention to a specific region of a molecule. Standard zooms often feel abrupt or force you…

When presenting complex molecular systems, timing is everything. Whether you’re walking students through conformational changes or preparing a highlight reel for a publication, controlling the flow of your animation can be the difference between clarity and confusion. One small, often…

Long hours spent designing, exploring, and visualizing molecular structures often mean long hours in front of a screen. If you’ve ever felt eye strain while working late into the evening in SAMSON, there’s a simple tweak that could make a…

It’s not uncommon for molecular modelers to encounter structures that are incredibly dense or complex. When working with large biomolecular assemblies or intricate materials, overlapping atoms and meshes can make it difficult to understand spatial relationships or highlight specific areas…

When working with complex molecular assemblies—especially during collaborative projects or presentations—ensuring that your visualizations are both clear and consistent can be surprisingly tricky. Different color schemes, inconsistent representations, and scattered visibility settings can all make it difficult for collaborators to…

Creating realistic membrane-protein systems is often a prerequisite in molecular dynamics simulations, but it can take time to carefully place lipids around a protein, avoid clashes, and ensure appropriate orientation. The Molecular Box Builder extension in SAMSON helps solve this…

When preparing scientific presentations or educational videos, molecular modelers often face a challenge: how to visually introduce complex molecular structures in a way that feels fluid and intuitive to viewers. A sudden jump from an empty scene to a fully…

When running molecular dynamics simulations with GROMACS, especially for complex biomolecular systems, precise atom or residue selection is often critical. Whether you’re setting up pull groups, performing umbrella sampling, or analyzing specific regions of your system, custom index groups can…

One common challenge in molecular modeling is the accurate orientation of molecular fragments when building new structures. Whether you’re assembling molecules from functional groups or trying to connect pre-defined assets, misaligned fragments can lead to structural errors that require time-consuming…