Author: OneAngstrom

If you’re working in molecular modeling, you’re likely juggling various file formats—PDBs from protein databases, XYZs from quantum chemistry, CIFs from crystallography, and many more. Each software tends to have its own preferred formats, making compatibility an ongoing concern, especially…

If you’ve ever spent hours perfecting a molecular animation or presentation in SAMSON, then you know how important it is to be able to share your work with your colleagues, your class, or your audience. But what’s the easiest way…

Creating clear and informative molecular visualizations can quickly become time-consuming—especially when dealing with complex systems like protein-ligand complexes, membrane assemblies, or large macromolecular structures. If you’ve ever found yourself spending more time setting up your visual representations than analyzing your…

When you’re creating molecular animations, there are moments when simply making an atom vanish instantly feels abrupt or visually jarring. Whether you’re teaching, presenting, or designing a publication-ready visual, gradual transitions can significantly improve clarity and storytelling. One frequently encountered…

Protein-protein docking can be challenging. One common frustration for molecular modelers stems from the abundance of false-positive predictions—docking orientations that score well but are biologically implausible. These often result from exploring a search space that’s too broad. Fortunately, the Hex…

When preparing molecular presentations or scientific movies, clarity and pacing are essential to focus your audience’s attention. One common challenge is how to introduce molecular structures visually without overwhelming viewers with sudden displays. If you’re working with detailed models—like proteins…

Working with systems that involve multiple copies of the same protein is increasingly common in coarse-grained molecular dynamics simulations — especially when simulating crowded environments or modeling self-assembly. Tools like Martinize2 help generate coarse-grained (CG) topologies for the MARTINI force…

Creating accurate molecular models of carbon nanotubes (CNTs) can be time-consuming—especially when you want a specific chirality, direction, or length. Manually inputting parameters is precise, but sometimes inspiration is better expressed visually. If you’ve ever found yourself wishing you could…

In molecular simulations, tracking the motion of binding partners, domains, or other parts of a system can quickly become overwhelming. Many molecular modelers manually inspect coordinate files or visualize entire trajectories, making it difficult to focus on the actual motion…

In molecular modeling, visual clarity matters—especially when you’re dealing with complexes where molecules interact closely, such as in docking studies or protein-ligand interactions. If you ever presented your model and found yourself thinking, “I wish I could just show how…