One common challenge faced by molecular modelers is juggling multiple specialized tools—often standalone or with limited interoperability. Researchers may rely on external executables, web services, or legacy codebases without an easy way to incorporate these within an interactive modeling environment.…

When modeling protein interactions or designing molecular assemblies, understanding symmetry isn’t just aesthetic—it’s functional. Whether you’re reconstructing biological assemblies or exploring interface contacts, sometimes protein crystal structures only show part of the picture. That’s where symmetry mates come in. In…

When working with complex molecular systems, visual clarity can be the difference between insight and confusion. Yet, customizing molecular representations for each project can become time-consuming — especially when switching between different systems or presentation styles. This is where Visual…

When working with protein conformations and transitions, one frequent source of frustration is a seemingly cryptic error message: “Cannot proceed because the structure does not make one connected component.” If you’ve encountered this in SAMSON while running ARAP interpolation, you’re…

In molecular modeling, clear communication is often as critical as the underlying data. Whether you’re presenting a molecular mechanism to a team or preparing instructional material for students, animations can bring clarity to complex structures. However, anyone who has tried…

When working on molecular models in SAMSON, you may have noticed that only one editor can be active at any time. This might appear limiting at first glance, especially to new users. Yet, it’s actually a design choice that simplifies…

One of the frequent challenges in molecular modeling is generating clean, structured data for reaction coordinate analysis. Whether you’re conducting free energy calculations or preparing enhanced sampling inputs, extracting the atomic positions of a ligand along a transition path is…

Running molecular dynamics simulations on a single system is already a complex task, but what happens when you want to simulate a whole set of conformations? For example, you might have generated different poses from a docking study, explored normal…

For many molecular modelers, scripting is both a blessing and a hurdle. Python unleashes the full potential of advanced modeling workflows, but coding from scratch—especially for simple, repetitive tasks—can slow down everyday work. Wouldn’t it be great to just describe…