Author: OneAngstrom

When setting up molecular dynamics simulations involving pulling—like center-of-mass (COM) pulling—it’s easy to overlook a crucial step: properly defining the simulation box. Yet, neglecting this may lead to artifacts caused by interactions with periodic images of the pulled molecule. If…

If you’ve ever looked at your molecular model and thought, “Something about the image feels flat,” you’re not alone. Depth perception is essential for interpreting the spatial relationships in molecular structures. But sometimes, even beautifully constructed 3D models fall short…

As molecular modelers, we often rely on color to highlight important structural features, differentiate between chains, identify atom types, or signal changing properties across trajectories. But here’s a common challenge: how do you choose a color palette that’s both visually…

Communicating molecular structures through visuals can be powerful—but only when the camera moves just right. Whether you’re building an academic presentation, making a video tutorial, or preparing content for publication, an awkward or static camera movement can detract from your…

When preparing molecular animations or presentations, it’s common to need fine control over which parts of your model are visible at specific moments. Whether you’re explaining a ligand binding site, highlighting a subunit, or focusing attention step-by-step during a conformational…

Communicating how molecules come together can be a real challenge for molecular modelers. Whether you’re creating a teaching aid, preparing a presentation, or simply trying to highlight structural organization in a molecular system, the ability to animate the assembly process…

When preparing animations of molecular models, one of the most common challenges is producing smooth vertical camera motions that enhance understanding without distracting the viewer. For example, you may want to show a ligand slowly approaching a binding pocket, or…

Generating biologically realistic environments for membrane proteins is often a challenge in molecular modeling. One frequent task is preparing a lipid bilayer around a protein to simulate its behavior in a membrane-like system. Traditionally, this requires time-consuming scripting or the…