Author: OneAngstrom

When working with complex molecular structures in SAMSON, one common challenge is how to optimize just a specific region of a molecule without affecting the rest. This need arises frequently—whether you’re focusing on docking sites, local defects, or studying the…

Presenting complex molecular mechanisms through visual animations can be a powerful way to communicate scientific insights. But sometimes, it’s not easy to find the right kind of motion to emphasize specific spatial relationships or draw attention to molecular groups. In…

Modeling carbon nanotubes (CNTs) is a common yet often tedious task in molecular design and materials science. Whether used for simulations in electronic properties, nanodevices, or biomolecular systems, building precise CNT structures can be surprisingly error-prone and time-consuming—especially if done…

One common challenge in molecular modeling is clearly and effectively communicating molecular motion, such as during simulations, conformational transitions, or reaction pathways. Capturing not just static snapshots but smooth transitions between molecular states is crucial for interpretation and presentation. If…

Protein docking simulations can be time-consuming, especially when you’re working with large biomolecular systems or exploring vast conformational spaces. A common struggle among molecular modelers? Waiting for docking runs that search everywhere when the relevant binding site is already known.…

When visualizing large molecular systems, presenting your scenes effectively—whether for a publication or a simple walkthrough—can make a big difference in communication. A common situation many molecular modelers face is the need to guide viewers from a broad view to…

One of the biggest challenges in molecular modeling is accurately perceiving spatial relationships between atoms and structures, especially in complex biomolecules. When depth perception is poor, it’s easy to misinterpret interactions, miss structural features, or create visualizations that are unclear…

If you’ve ever juggled multiple molecular models in a single project, you probably know the feeling: disorganization creeping in, files multiplying, structures getting lost in visual noise, and selections becoming harder to manage. A structured environment can make a big…

During molecular modeling, geometry optimization is a crucial step for refining structures prior to simulation or analysis. SAMSON’s implementation of the FIRE (Fast Inertial Relaxation Engine) minimizer helps you accelerate this process. But what happens when atoms are moved manually…