Sometimes, as a molecular modeler, you run into compatibility issues with datasets, specific extensions, or institutional setups that make it necessary to use an older version of your favorite simulation platform. If you’re using SAMSON, the integrative molecular design platform,…

Presenting complex molecular mechanisms to collaborators, students, or within publications often requires far more than static images. But creating dynamic, high-quality animations can be time-consuming, especially if it involves coding or video editing tools unfamiliar to most molecular modelers. If…

One of the most common frustrations when working with molecular systems is the time and effort it takes to get a clear, informative visualization. Whether you’re showcasing a protein-ligand interaction, analyzing docking results, or preparing images for publication, manually adjusting…

One common stumbling block when modeling conformational transitions in proteins is making sure your start and goal structures are properly defined—and actually compatible with each other. If the structural data going into your simulations isn’t prepared consistently, your modeling pathways…

Managing molecular models often means juggling multiple molecules, properties, and hierarchies within a single project. For many researchers and modelers, the challenge lies in keeping track of what’s loaded, what’s selected, or how different parts of a molecule are related.…

When presenting molecular simulations or structural results, small visual choices can significantly impact how viewers perceive your work. One subtle yet powerful way to guide attention and make transitions smoother is by using background animations to switch between scenes. In…

Modeling conformational transitions is central to understanding biomolecular function. But once paths between protein conformations are computed, how can you quickly analyze them and communicate the results? This post offers a practical look at how to visualize and interpret transition…

Creating high-quality molecular animations often requires more than just rotating around a molecule. Sometimes, we want to elevate the entire viewpoint smoothly in a vertical direction—think of showcasing a molecular complex from bottom to top, or emphasizing structural features along…

Running molecular dynamics simulations on large biomolecular systems can be a real challenge when your local computer lacks the necessary computational power. Crashes, long processing times, and limited storage are common issues that slow down research workflows. What if you…