Molecular modeling projects often involve creating visual presentations to highlight specific interactions, regions of interest, or structural changes. But when a model is too complex, clutter from surrounding atoms can obscure what really matters. If you’ve ever struggled to focus…

If you’re working in molecular design or drug discovery, you’ve probably come across the need to explore structural analogs of a lead compound – whether to improve binding, reduce toxicity, or evade metabolic vulnerability. Traditionally, this can require manual editing…

When setting up molecular dynamics (MD) simulations using coarse-grained (CG) models, one recurring issue modelers face is improper solvation: water molecules overlapping with solute atoms or each other. This can happen easily when using default settings that are not tailored…

When creating molecular animations, one frequent challenge is controlling when specific components appear during your presentation. Whether you’re highlighting a ligand binding to a protein or the formation of a molecular assembly, the timing of element visibility is essential to…

When working with proteins, even a single poorly-placed residue can make the difference between a stable simulation and a failed model. For molecular modelers, quickly identifying and fixing conformational outliers is more than just helpful – it’s essential. But in…

Molecular modelers often struggle with one recurring challenge: visual clarity. Whether you’re preparing figures for a publication, a presentation, or simply trying to interpret complex systems more clearly, the way molecules are rendered can have a huge impact on your…

Visualizing molecular transitions is a fundamental part of molecular modeling. Whether you’re tracking a conformational change, reviewing a reaction pathway, or simply cycling between states, being able to loop animations smoothly—and sometimes in reverse—can make a big difference. In SAMSON,…