Author: OneAngstrom

When working with complex molecular structures, one common challenge is understanding the spatial relationships between different parts of a model. Proteins, ligands, and assemblies can quickly turn into a dense visual web where depth becomes hard to interpret. A powerful…

In drug design and molecular optimization, exploring structural variants of a given parent molecule is a common strategy to improve activity, solubility, or other properties. Manually generating all these variants, however, can be repetitive and error-prone—even before simulations begin. The…

For molecular modelers using the SAMSON platform, organizing and turning the right features on or off at the right time can save both time and computational resources. Whether you’re switching between different projects, collaborating in a team, or simply exploring…

When working with large macromolecular complexes—such as viral capsids or multi-subunit protein assemblies—molecular modelers often encounter one frustrating question: What symmetry best represents this structure? Identifying the correct symmetry group is not just about visualization—it’s about improving the quality and…

Understanding how defects impact the properties of crystalline materials is a crucial task for materials scientists, physicists, and molecular modelers. Defects in crystal lattices can significantly affect mechanical strength, conductivity, optical behavior, and other physical properties. However, visualizing and simulating…

One of the most common challenges faced by molecular modelers is visualizing changes in molecular conformations over time. Whether you’re working with molecular dynamics (MD) simulations, conformational sampling, or interactive modifications, seeing how a system evolves in space and time…

When preparing biological systems for molecular dynamics simulations, one recurring pain point is deciding what to do with water molecules. Should you delete all of them? What if some are tightly bound and essential for protein function or ligand binding?…

When creating animations of molecular systems, you’re often focused on illustrating detailed transitions—like conformational changes, ligand docking, or energy minimizations. But there’s a subtle issue that many researchers encounter: the camera viewpoint can drift between frames unintentionally, especially if no…