Author: OneAngstrom

For many molecular modeling tasks, especially those involving large biological assemblies like viral capsids or protein complexes, understanding molecular symmetry can save time and reduce complexity. But automatic symmetry detection isn’t perfect—sometimes, you already know the answer, and it’s best…

Have you ever wanted to create a smooth camera flyby around a molecular structure but felt overwhelmed by animation timelines or manual camera scripting? If you’re a molecular modeler trying to present your system in a visually engaging way—for a…

When working on complex molecular structures in SAMSON, navigating efficiently between different viewpoints can significantly improve your productivity and understanding of the system. Whether you’re analyzing binding pockets, exploring lattice arrangements, or reporting structure-function relationships, switching views without hassle is…

Molecular dynamics (MD) simulations often require targeted control or analysis of specific parts of a structure—for example, calculating forces on side chains, analyzing water clusters, or applying constraints to ligand atoms. GROMACS automatically generates standard atom groups (like Protein, Water,…

Designing DNA nanostructures is only half the task for molecular modelers interested in simulations. Once the geometry is ready, the challenge becomes how to export that design for computational analysis. If you work with coarse-grained molecular dynamics, you’re likely using…

In molecular modeling, clarity is key. Whether you’re presenting a simulation, building an educational video, or simply exploring complex biomolecular structures, drawing attention to specific components while minimizing distractions can greatly improve communication. One common challenge modelers face is how…

Setting up a coarse-grained (CG) system for molecular dynamics simulations can save time and computational resources, but comes with its own challenges. One such challenge — often overlooked by beginners — is related to how solvent molecules are added to…

When working on molecular simulations or structural rearrangements, animation workflows can become repetitive and time-consuming. A common challenge for molecular modelers is ensuring that once they achieve the right animation involving atom movements—for example, docking, simulated dynamics, or manual manipulation—they…

One of the constant challenges faced by molecular modelers is simplifying complex molecular scenes for presentations or animations. Whether it’s to highlight a reaction site, declutter overlapping strands, or direct attention to a specific structure, controlling visibility is a key…