When working with protein structures, it’s common to begin with asymmetric units from the Protein Data Bank (PDB). However, research and design tasks like analyzing quaternary structures, identifying protein-protein interfaces, or building full biological assemblies often require the generation of…

In many molecular simulations, especially when studying aggregation, crowding, or system size effects, researchers need to work with several replicas of the same protein. However, preparing these multi-replica systems for coarse-grained (CG) simulations can be a tedious and error-prone process—especially…

When you finally get that perfect view of your molecular model — maybe a key binding pocket, an optimized ligand pose, or a nicely minimized structure — you probably want to save it as a high-quality image. But the default…

Sometimes, as a molecular modeler, you run into compatibility issues with datasets, specific extensions, or institutional setups that make it necessary to use an older version of your favorite simulation platform. If you’re using SAMSON, the integrative molecular design platform,…

Presenting complex molecular mechanisms to collaborators, students, or within publications often requires far more than static images. But creating dynamic, high-quality animations can be time-consuming, especially if it involves coding or video editing tools unfamiliar to most molecular modelers. If…

One of the most common frustrations when working with molecular systems is the time and effort it takes to get a clear, informative visualization. Whether you’re showcasing a protein-ligand interaction, analyzing docking results, or preparing images for publication, manually adjusting…

One common stumbling block when modeling conformational transitions in proteins is making sure your start and goal structures are properly defined—and actually compatible with each other. If the structural data going into your simulations isn’t prepared consistently, your modeling pathways…

Managing molecular models often means juggling multiple molecules, properties, and hierarchies within a single project. For many researchers and modelers, the challenge lies in keeping track of what’s loaded, what’s selected, or how different parts of a molecule are related.…

When presenting molecular simulations or structural results, small visual choices can significantly impact how viewers perceive your work. One subtle yet powerful way to guide attention and make transitions smoother is by using background animations to switch between scenes. In…