Visualizing molecular transitions is a fundamental part of molecular modeling. Whether you’re tracking a conformational change, reviewing a reaction pathway, or simply cycling between states, being able to loop animations smoothly—and sometimes in reverse—can make a big difference. In SAMSON,…

When modeling molecular interactions, demonstrating a ligand binding to a receptor is essential. But what about the reverse process? Undocking animations are just as important, especially when preparing presentations, educational content, or investigating energy release during the unbinding stage. In…

Whether you’re analyzing protein-ligand interactions or checking geometry optimization results, measuring precise atomic distances is a routine—but vital—task in molecular modeling. Yet, for many users, keeping track of those measurements or quickly accessing the most relevant ones can be frustrating…

One of the recurring challenges in modeling protein conformational transitions is obtaining realistic motion pathways without having to simulate every single atom in the structure. Experienced molecular modelers know that involving too many atoms can be computationally expensive, while ignoring…

When preparing scientific presentations or educational videos using molecular models, one of the common challenges is selectively focusing the viewer’s attention on specific parts of a system. For molecular modelers and educators alike, this often means finding a way to…

When preparing molecular animations for presentations or educational content, it’s often necessary to emphasize specific parts of a system only for a short duration. Whether it’s highlighting a binding site, showing ligand entrance, or drawing attention to transient structures, controlling…

One of the biggest challenges faced by molecular modelers today is finding the right combination of tools without switching constantly between different software environments. If you’ve ever wished for a seamless way to expand your modeling capabilities directly within your…

Finding saddle points and minimum energy paths (MEPs) between molecular conformations can be computationally expensive. The Parallel Nudged Elastic Band (P-NEB) method in SAMSON is designed to optimize such transitions by refining intermediate images along a proposed path. But depending…

When modeling conformational transitions in proteins, small details can lead to big differences in results. One frequently overlooked step is proper energy minimization before running any transition pathway planning. Skipping this step can introduce artificial forces, limit convergence, or worse…