Author: OneAngstrom

When working with protein structures from the Protein Data Bank (PDB), you often start with an asymmetric unit — just a portion of the full biological or crystallographic assembly. While this is sufficient for some analyses, many modeling and simulation…

Predicting how molecules transition from one state to another is at the heart of molecular modeling. Whether you’re studying protein folding, ligand binding, or conformational changes, knowing the minimum energy path (MEP) between two states can shed light on kinetics…

If you’ve ever tried installing scientific software in a university or institutional setting, you’ve likely run into a familiar obstacle: you don’t have admin rights. Maybe you’re working on shared lab computers, maybe IT is hard to reach, or maybe…

Anyone working in molecular modeling knows that navigating structural complexity is part of daily life. Whether building a model from scratch or modifying existing biomolecules, the ability to interactively edit molecular systems in a flexible, precise manner can dramatically reduce…

For many molecular modelers and cheminformatics researchers, going from a simple SMILES string to a complete 3D structure can involve cobbling together multiple tools, scripts, or web platforms. This can be time-consuming and disrupt workflow—especially when working with large datasets.…

Building carbon nanotube (CNT) models is often a central need in molecular modeling, nanoscience, and materials simulation. Whether you’re designing CNT-based sensors, creating nanostructures for simulations, or exploring their mechanical and electronic behavior, the ability to quickly and intuitively generate…

If you’ve ever created a molecular animation and noticed that the camera angle changes unexpectedly between frames — even though you didn’t mean to animate it — you’re not alone. This can be frustrating, especially when you want a specific…