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…

Molecular modelers working with carbon nanotubes (CNTs) often need precise control over nanoscale parameters. Whether you’re modeling molecular transport, exploring electronic properties, or constructing nanoelectromechanical systems (NEMS), the geometry of your nanotubes matters. One common challenge is reproducibly designing CNT…

One of the most common scenarios in molecular modeling is embedding a membrane protein into a lipid bilayer. While it sounds straightforward, anyone who has tried to manually position hundreds of lipids around a protein knows this can be a…

One challenge that comes up again and again in molecular modeling is how to clearly communicate structural insights to others. Whether you’re preparing a presentation, building a tutorial, or creating a publication-quality video, controlling the camera’s motion is essential. This…

Molecular modeling often requires performing highly specialized simulations, visualizations, or data workflows—tasks that might not be fully covered by existing tools. This gap frequently leads scientists and developers to create their own scripts or pipelines. But wouldn’t it be more…

Visual presentation is a critical aspect of molecular modeling, especially when preparing demonstrations, tutorials, or research presentations. One common challenge faced by molecular modelers is how to control the visibility of atoms, molecules, or annotations in a smooth and convincing…