Author: OneAngstrom

Molecular simulations often involve tracking complex atomic rearrangements: docking events, folding pathways, or drug interactions. But replaying those subtle moves isn’t always straightforward. If you’ve ever needed a clean, visual representation of how atoms moved throughout a simulation for presentations…

Molecular modelers often face a recurrent frustration when studying large biomolecular structures: the lack of dynamic, visual insight into conformational transitions. This is particularly true for complex glycoproteins like the SARS-CoV-2 spike protein, which plays a central role in viral…

When preparing a molecular animation—for a presentation, a class, or a social media post—clarity is everything. Visual clutter, overlapping elements, or sudden disappearances can distract your audience and cloud your key message. This is especially true when you want to…

If you’ve ever tried to work with molecular structures from a variety of sources, you’ve likely faced the challenge of incompatible file formats. Maybe you received data from a collaborator in a format your tool doesn’t recognize. Or perhaps you…

Molecular modelers often face challenges when presenting their research effectively—especially when trying to integrate molecular scenes with presentation elements like background slides or contextual imagery. In team meetings, research talks, or teaching, conveying your message clearly and attractively matters. This…

When performing molecular dynamics simulations involving center-of-mass (COM) pulling, failing to correctly define the simulation box can lead to artifacts—especially when periodic boundary conditions come into play. One common challenge molecular modelers face is ensuring that enough space exists in…

If you’ve ever prepared a molecular presentation and wanted to clearly show a ligand docking into a receptor, you may have run into a common challenge: animating the motion in an intuitive, visually appealing way—without spending hours tweaking coordinates or…

When working with molecular models, one common step before running simulations or analyses is geometry optimization. This ensures that your structure starts from a relaxed configuration, typically corresponding to a local energy minimum. In SAMSON, an integrative platform for molecular…