Author: OneAngstrom

A molecular structure can look ready for simulation and still contain details that complicate preparation: alternate atom locations, waters you do not need, small molecules without topology parameters, or monatomic ions left over from the structure. Removing everything that looks…

A distance or angle can look correct in one snapshot and change as soon as you move atoms or minimize a structure. That makes it easy to lose track of whether a geometric feature is still what you intended to…

Moving atoms in a molecular model can expose a frustrating limitation: the structure may need to form or break bonds, but a simulation that assumes a fixed topology cannot adapt as you edit. Interactive Modeling Universal Force Field (IM-UFF) is…

A molecular structure can be difficult to understand from a single viewpoint. A carefully framed orbit can reveal how parts of an assembly relate in three dimensions—but an orbit that circles the wrong point or moves through an unhelpful plane…

A protein–ligand structure can contain many nearby atoms, but a 3D view does not always make it easy to see which residues are close to a ligand or how the contacts are arranged. Switching between the structure and notes can…

A molecular structure can look reasonable on screen and still be a poor starting point for an energy calculation. The selected model task may not match the system, a molecule’s charge or spin may be wrong, or a periodic cell…

A molecular model can contain several chains, residues, interaction regions, or data values—and color is often the quickest way to tell them apart. It is also easy for color to create confusion: a smooth gradient may imply an ordered scale…

A molecular group can change its overall shape without an obvious change in its size. It may become more elongated or otherwise less sphere-like while its radius of gyration stays similar. If you are comparing structures along a path or…

When you inspect a molecular trajectory, a common question is not just what changed? but which combinations of changes appeared most often? Looking at two observables separately can hide that relationship. A distance may span a broad range, for example,…