Author: OneAngstrom

As molecular modelers, we often deal with complex structures, from proteins to nanomaterials. When visualizing these assemblies, color plays a critical role in separating elements, highlighting features, or simply making models easier to interpret. But selecting colors manually each time…

Collaborative molecular modeling projects often involve more than just structural data: Python scripts, research articles, experimental data, machine learning models, and various other resources contribute to replicability and transparency. But organizing and sharing these assets alongside complex molecular systems tends…

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…