Author: OneAngstrom

One common frustration for molecular modelers when using complex design platforms is tool overload: too many features enabled at once, leading to cluttered interfaces and unpredictable behavior. In SAMSON, this problem is addressed in a simple but effective way: at…

If you’ve ever attempted protein conformation interpolation in SAMSON using the ARAP Interpolator, only to be blocked by an error like “Cannot proceed because the structure does not make one connected component”, you’re not alone. Many molecular modelers encounter this…

When preparing molecular structures for simulations, one of the most common challenges is geometry optimization. Whether you’re refining protein structures, minimizing ligand conformations, or cleaning up imported molecular data, the goal is often the same: relax your structure to a…

If you work with molecular visualizations, chances are you’ve sometimes found it hard to understand the structure of crowded regions or complex folds. Molecules can often look flat or difficult to interpret—especially in ribbon or surface models where depth is…

Understanding how ligands move through binding pockets is vital in molecular modeling, whether you’re simulating binding/unbinding events, preparing free energy calculations, or simply visualizing molecular mechanisms. If you’ve ever computed a path (e.g., using a method like parallel nudged elastic…

If you’ve ever built a molecular animation to explain a structural transformation, introduce a conformational change, or visualize a docking sequence, you know how quickly things can move. For viewers—whether students, colleagues, or collaborators—absorption takes time. But what if your…

Creating realistic membrane-protein systems is a recurring challenge in molecular modeling. Membrane proteins play critical biological roles, but setting up simulations that combine them with appropriate lipid environments often involves multiple tools, file format conversions, and a fair amount of…