Author: OneAngstrom

If you’re a molecular modeler creating animations of complex molecular systems, you’ve likely run into this challenge: too many elements vying for attention in your scenes. Whether you’re showing conformational changes, reaction mechanisms, or protein-ligand interactions, excess visual clutter can…

When working with large protein complexes or viral capsids, understanding and leveraging their symmetry can significantly simplify your structural analysis and simulations. The Symmetry Detection extension in SAMSON automatically identifies possible symmetry groups in biological assemblies — but what happens…

If you’ve ever built coarse-grained (CG) models using the MARTINI force field and hit a frustrating error during topology generation, you’re not alone. One common cause? Non-unique residue and chain identifiers in systems that include multiple replicas. Fortunately, SAMSON makes…

Interactive simulation can be a game-changer when modeling molecules. Instead of building a molecular structure, launching a long simulation, and then checking the result, what if you could poke, prod, and drag atoms—and see in real time how the molecule…

Getting a protein ready for docking is often more time-consuming than the docking itself. Whether you’re preparing for virtual screening or structural analysis of complexes, the cleanup step is crucial. Missing hydrogens, alternate atom positions, leftover water molecules—these details can…

Designing carbon nanotubes manually in molecular modeling platforms can be a slow and repetitive process. If you’ve ever painstakingly duplicated and aligned atomic rings to form tubes, you know how tedious it can get—especially when you’re aiming for atomic precision…

In molecular modeling and dynamics, visual clarity is essential. Whether you are preparing a scientific presentation, illustrating a complex conformational change in a biomolecule, or creating an educational video, the ability to orchestrate what appears—and when—can mean the difference between…

When modeling conformational transitions between protein states, one of the most overlooked yet crucial steps is structure preparation. Whether you’re setting up umbrella sampling, visualizing intermediate states, or refining with steered molecular dynamics, how you prepare your structures can determine…

When presenting or analyzing complex molecular systems, one common challenge is visual clutter. Protein assemblies and large biomolecular structures often appear as dense blocks where important elements can be hidden or hard to distinguish. If you’ve ever struggled to present…

When setting up calculations for reaction coordinates or preparing data for free energy profiling, researchers often find themselves in need of atomic coordinate files at multiple points along a ligand’s movement path — usually in PDB format. Doing this manually…