Author: OneAngstrom

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,…

When you’re building molecular models, clarity is everything. Whether you’re preparing a presentation, creating an educational resource, or documenting complex systems, annotations and visual cues can make your work much more effective. One underused but essential feature in SAMSON is…

Analyzing protein–ligand interactions is a key step in molecular modeling and drug design. Whether you’re a student, researcher, or experienced computational chemist, you’ve probably found yourself trying to figure out a fast and visual way to confirm whether your ligand…

In molecular modeling, attention to detail is everything. Whether you’re preparing a presentation, illustrating a mechanism, or crafting an educational video, highlighting specific structures—while letting others momentarily disappear—can improve clarity and focus. However, manually fading parts of a structure in…