Author: OneAngstrom

When working on molecular systems, being able to clearly communicate what you are seeing is just as important as understanding what you are looking at. Capturing smooth transitions for presentations, tutorials, or publications can be a challenge, especially when you…

When working on complex molecular systems — such as proteins with multiple ligands, solvated complexes, or multimeric structures — it’s common to revisit specific components repeatedly. Selecting a ligand, then moving to a receptor, and later examining water molecules or…

One common challenge in molecular modeling and visualization is keeping audiences visually engaged during presentations—especially when presenting static structures. While it’s easy to become absorbed in your own structural analysis, collaborators or students may struggle to connect with the material…

One of the most delicate steps in molecular simulation workflows is the NPT (isothermal-isobaric) equilibration phase. After energy minimization and temperature stabilization via NVT equilibration, the next goal is to ensure that your system reaches a stable density under the…

For many molecular modelers, clarity in visualization is more than aesthetic—it’s essential for understanding structure, function, and interaction. Whether you’re interpreting protein folding or preparing visual outputs for a publication, good molecular graphics save time and reduce risk of misinterpretation.…

Switching between different modeling tasks often means switching contexts — from analyzing molecular structures to preparing simulations or animating reactions. For molecular modelers, bouncing between tools and reconfiguring windows can waste valuable time and break focus. This is where SAMSON’s…

One commonly overlooked yet crucial step in modeling protein conformational transitions is setting up the sampling box. If you’ve struggled with generating relevant pathways or wondering why you’re getting unexpected motions, it’s likely that your sampling region is not well…

When building molecular models, effective visual distinction between different structures, chains, atoms, or datasets is essential for clarity. But how often have you found yourself stuck with default colors that just don’t work — whether they’re too similar to distinguish…

Finding ligand unbinding pathways can be complex, especially when accurate energy evaluations are essential to guide the search. If you’re using SAMSON’s Ligand Path Finder, correct setup of the energy model is a critical early step. In this post, we’ll…