Author: OneAngstrom

In molecular modeling, comparing protein structures is a frequent and essential task—whether you’re identifying conserved structural motifs, evaluating mutant effects, or building homology models. But what happens when you’re only interested in a specific structural feature, like an active site…

If you’re a molecular modeler running simulations in GROMACS, getting the system to the right density through NPT equilibration can feel more like black magic than science. Pressure is tricky. Density fluctuates. And running the same step several times feels…

If you work with multiple protein structures, you know the pain of repetitive cleanup tasks: removing water molecules, fixing alternate locations, adding hydrogens… doing it dozens of times is tedious, error-prone, and slows down your workflow dramatically. Luckily, if you’re…

When studying large biomolecular assemblies—such as viruses, protein complexes, or synthetic nanomaterials—symmetry isn’t just aesthetic. Identifying and understanding symmetry can help uncover repeated functional motifs, improve structural validation, and dramatically reduce computational demands. SAMSON’s Symmetry Detection extension brings powerful symmetry…

One of the key challenges faced by molecular modelers is effectively conveying spatial depth and structure in complex molecular scenes. Whether you’re presenting your work in a publication or simply trying to better understand a molecular structure, visual clarity can…

Collaborating on molecular modeling projects often means juggling email threads, cloud drives, file formats, and version mismatches. For molecular modelers, it can be frustrating to share large, complex structural data or simulation results in a streamlined and secure way—especially when…

Running umbrella sampling simulations to determine the Potential of Mean Force (PMF) is a common and powerful approach in molecular modeling. But once trajectories are produced, a recurring challenge is understanding how well the reaction coordinate space is sampled. Poor…

Preparing a molecular animation that accurately conveys a binding mechanism or illustrates structural complementarity is often more work than expected. Whether you’re crafting a visual to accompany a publication or designing an animated explainer for your lab website, manually placing…

Working with large and complex molecular systems can often feel overwhelming, especially when you’re trying to isolate a specific part of your model—ligands, active sites, or particular side chains—for editing, analysis, or visualization. If you’ve ever found yourself switching endlessly…

When presenting molecular systems to colleagues or students, clarity matters. You want to walk them through a complex structure without clutter, and focus their attention on specific regions. But abruptly hiding parts of a structure can be visually jarring—especially in…