When preparing scientific presentations or educational videos using molecular models, one of the common challenges is selectively focusing the viewer’s attention on specific parts of a system. For molecular modelers and educators alike, this often means finding a way to…

When preparing molecular animations for presentations or educational content, it’s often necessary to emphasize specific parts of a system only for a short duration. Whether it’s highlighting a binding site, showing ligand entrance, or drawing attention to transient structures, controlling…

One of the biggest challenges faced by molecular modelers today is finding the right combination of tools without switching constantly between different software environments. If you’ve ever wished for a seamless way to expand your modeling capabilities directly within your…

Finding saddle points and minimum energy paths (MEPs) between molecular conformations can be computationally expensive. The Parallel Nudged Elastic Band (P-NEB) method in SAMSON is designed to optimize such transitions by refining intermediate images along a proposed path. But depending…

When modeling conformational transitions in proteins, small details can lead to big differences in results. One frequently overlooked step is proper energy minimization before running any transition pathway planning. Skipping this step can introduce artificial forces, limit convergence, or worse…

Preparing membrane-protein systems for simulation is a task that molecular modelers regularly face, especially when modeling transmembrane proteins. However, manually inserting lipids and ensuring proper alignment around a protein can be time-consuming and error-prone. If you’ve ever tried to construct…

Molecular modeling often requires precise visualization to communicate structural insights clearly — whether in academic papers, presentations, or team meetings. But framing your molecular system from the right angles can be time-consuming, especially if you’re repeatedly adjusting views to get…

Running umbrella sampling simulations is only part of the story in calculating a Potential of Mean Force (PMF). A common challenge molecular modelers face is realizing—too late—that parts of the reaction coordinate space were not well covered, leading to unreliable…

One of the most common frustrations in molecular modeling is constantly reconstructing the same types of visualizations: highlighting ligands, showing ribbons for proteins, zooming in on active sites, choosing color schemes, and setting up camera perspectives. When models become complex,…