Creating realistic models of nanostructures like carbon nanotubes (CNTs) can be time-consuming and technically complex. For molecular modelers and materials scientists, the ability to rapidly generate customizable CNTs is often crucial for prototyping device components, performing simulations, or illustrating theoretical…

Struggling with presenting complex molecular scenes in a clean, digestible way? If you often build animations to showcase conformational changes, protein-ligand interactions, or intricate visualizations involving multiple overlapping layers, you’ve probably asked yourself: How do I control what’s visible and…

Controlling how molecular structures appear over time can significantly enhance the clarity and flow of molecular animations. This is especially true when presenting to an audience or building an educational video. A common challenge, however, is managing the progressive appearance…

For molecular modelers working with large biomolecular structures, navigating between residues in 3D can quickly become a tedious task. Zooming, panning, rotating – and still not finding that specific residue you were looking for. Sound familiar? Fortunately, SAMSON offers a…

When working on complex molecular modeling projects, researchers often need specific tools tailored to their workflows. One common challenge? Quickly finding and managing the right computational modules without interrupting your progress. That’s why flexible software like SAMSON—with customizable add-ons called…

Creating scientific animations of molecular systems can be time-consuming, and even experienced modelers sometimes face challenges with accurately communicating dynamic behaviors. One common pain point many encounter is smoothly moving atoms or molecular fragments across frames without introducing artifacts or…

As molecular systems grow in size and complexity, adding labels to specific atoms, residues, or molecules can be a great way to identify and present the most relevant parts of your structure. However, it’s easy for labels to become overwhelming,…

Preparing ligands for docking can feel like a minor step, especially when your molecular modeling workflow is already complex. But overlooking ligand minimization can lead to misleading docking results and longer computation times. In this blog post, we’ll walk through…

For researchers in molecular simulation, computing Potential of Mean Force (PMF) profiles can be an involved task—especially when dealing with data from multiple umbrella sampling simulations. Manual WHAM (Weighted Histogram Analysis Method) workflows in GROMACS often require scripting, data formatting,…