Author: OneAngstrom

When building, comparing, or preparing molecular models for visualization or simulation, one common issue faced by modelers is the orientation and relative positioning of molecular structures. Misaligned molecules can complicate analysis, generate cluttered views, and obstruct accurate measurements or transformations.…

Understanding how your ligand interacts with a receptor at the atomic level is key to rational drug design. However, many molecular modelers spend a surprising amount of time just trying to generate clear, informative visuals of binding sites. If you’re…

When visualizing complex molecular systems, spatial perception plays a crucial role. You need to know what atom is behind or in front, how close molecular structures are to each other, and how everything fits together in 3D space. But sometimes,…

When working on complex molecular systems, navigating between multiple regions of interest can feel like a never-ending exercise in reselecting atoms, residues, or molecules. Whether you’re switching between a ligand, several candidate binding sites, or parts of a large biomolecular…

If you’ve ever tried to present complex molecular structures or chemical processes in a clear and engaging way, you probably know how difficult it can be to explain spatial relationships or dynamic transformations with just static images. Whether you’re preparing…

One of the most common challenges in molecular dynamics is getting simulations up and running across different computing environments. If you’ve ever struggled to compile GROMACS, wrestled with queuing systems, or managed large sets of input files on remote machines,…