Presenting molecular structures to others can be a challenge, especially when static images fail to capture important spatial relationships and behavior. Whether you’re teaching, preparing a publication, or simply sharing a beautiful molecular system with your colleagues, clarity often lies…

Anyone working with biomolecular simulations knows the drill: you fetch a structure from the Protein Data Bank and it comes with water molecules — hundreds of them, sometimes thousands. The big question is: which ones should you keep? In many…

When you’re presenting molecular models, particularly during a talk, an animation, or even while creating educational videos, it’s important to guide your audience’s attention to certain structures without overwhelming them. One common challenge molecular modelers face is how to make…

As a molecular modeler, you’ve likely faced slow structural relaxation in systems with collective motions—especially when preparing simulations or refining models after manual manipulations. If you’ve used the steepest descent algorithm and watched the energy barely drop while your patience…

Setting up molecular simulations can be frustratingly complex, especially when you’re trying to model systems that undergo structural changes. In many tools, altering bonds or atom types mid-simulation requires stopping, resetting, and restarting the entire process. That’s a workflow killer.…

When analyzing molecular structures or simulating systems over time, researchers often encounter the challenge of maintaining focus on a specific region of interest while the rest of the system evolves. Maybe you’re observing a binding site, an active center, or…

When working with large protein assemblies, viral capsids, or nanostructures, modeling every atom individually becomes computationally expensive. Fortunately, many of these systems exhibit internal symmetry—a pattern that can be leveraged to simplify simulations. SAMSON’s Symmetry Detection app automatically finds symmetry…

Molecular modelers often work on multiple structures simultaneously—preparing systems, analyzing interactions, or designing new molecules. But managing these workflows effectively can be challenging. You might find yourself juggling several PDBs and simulations, switching back and forth between them to cross-reference…