A protein–ligand pose can look convincing in 3D and still be difficult to review. Atoms overlap visually, important contacts are buried, and explaining what is near the ligand often means repeatedly switching between views. An interaction diagram can make that…

You have a molecular structure framed just right: a close-up for inspecting a region, perhaps, or a full view that shows how the pieces fit together. Then you navigate elsewhere, and the view you wanted is gone. Recreating a useful…

A simulation box can look like a simple container around a molecule. But with periodic boundary conditions, the box is repeated in every direction: a molecule can effectively interact with copies of itself. If the box is too small, those…

A production molecular dynamics run is where a prepared system begins generating the trajectory you will later inspect and analyze. Yet the transition from equilibration to production is an easy place to lose time: the wrong input may be selected,…

Moving an atom by hand can be a quick way to explore a molecular structure—but it can also leave you wondering whether the rest of the molecule will respond sensibly. Interactive modeling offers a way to manipulate atoms while a…

A molecular structure can look ready for calculation and still produce confusing results: the wrong task is selected, a molecular charge is left at its default, or the first energy reading has not appeared yet. These are easy details to…

Manually selecting atoms to isolate a region of a crystal or molecular structure can be slow and imprecise. The problem becomes more noticeable when the boundary is curved: clicking atom by atom rarely produces a clean circle, sphere, or other…