Author: OneAngstrom

When preparing biological systems for molecular dynamics simulations, one recurring dilemma is deciding which water molecules to keep—and which to remove. Some crystal waters are tightly bound or functionally important, especially in active sites. Others are just noise, cluttering your…

If you’re working with coarse-grained (CG) systems using the MARTINI force field, you’ve probably encountered unexpected issues when solvating your system. Molecules may appear too close to each other, or your system might behave strangely during simulation setup. A common…

When preparing molecular presentations, many scientists struggle with delivering complex results clearly and engagingly. A frequent challenge is: how to create smooth, visually coherent transitions between scenes, especially when contextual images like presentation slides or textures are needed in the…

Long hours spent visualizing and designing molecular structures might look exciting, but they also come with a common downside: eye fatigue. If you work during late hours or in environments with low ambient light, the default bright interface of many…

Color can make or break the interpretation of molecular models. For researchers and designers working in molecular science, the right color palette isn’t just aesthetic—it’s essential for accurate, effective communication. Whether you’re analyzing large biomolecular systems or visually presenting molecular…

When working with protein structures from the Protein Data Bank (PDB), you’ll often find yourself looking at what’s called the asymmetric unit. This is just one portion of the complete biological assembly — the full, functional form of the protein,…

Setting up realistic presentations of molecular interactions often involves visualizing molecules transitioning between docked and undocked states. Whether you’re demonstrating a ligand leaving a binding pocket, or separating structural elements for clarity, precise control over these animations can make your…

Sharing research data and molecular models with colleagues is essential to collaborative science. But in many cases, molecular modelers face challenges when it comes to managing who can see, access, or edit their files—especially when those files are hosted in…

When creating presentations or tutorial videos in molecular modeling, clarity and flow are critical. One common challenge is controlling when specific molecular structures appear, particularly when building complex animations step-by-step. Simply adjusting transparency can make objects hard to see or…

When working with large molecular systems, one of the biggest challenges is the efficient and precise selection of atoms for modification, visualization, or interaction. Whether you’re building nanoscale structures or simply preparing regions for simulation or analysis, complex selections based…