When creating molecular presentations, clarity and visual appeal are key. Molecular modelers often need to explain complex mechanisms, compare conformational states, or guide an audience through molecular interactions. But managing visual transitions between slides or images in a molecular visualization…

Preparing ligands for docking is a common task for molecular modelers, but it often raises a recurring question: should I minimize my ligands before docking? Poor ligand geometries can hinder docking accuracy or even prevent successful pose generation. If you…

One of the recurring challenges in molecular simulations is running the same workflow multiple times for a set of slightly different initial conformations. Whether you’re sampling alternative ligand binding poses, scanning mutations, or simply running simulations from different frames of…

When you’re crafting a molecular animation—perhaps to highlight a binding site, depict a conformational change, or simply help your peers better understand motion in a protein—it’s not always about rotating or dragging atoms. Sometimes, you just want a subtle, naturalistic…

One challenge molecular modelers frequently face is ensuring that their system reaches a stable temperature before proceeding to production molecular dynamics simulations. This step — known as NVT Equilibration — is crucial to achieve meaningful simulation results. It sounds straightforward…

When dealing with large macromolecular assemblies in structural biology, it is common to encounter multiple plausible symmetries within a single structure. Whether you’re simulating a viral capsid or designing symmetric nanomaterials, selecting the correct symmetry group can streamline your workflow…

Understanding protein conformational changes can be both technically challenging and crucial for molecular modelers, especially in the context of drug design and protein-ligand interaction predictions. One such key conformational transformation is the opening movement of the SARS-CoV-2 spike protein—a process…

For molecular and materials modelers, reproducing realistic structural behaviors of crystals is essential for accurate simulations. One recurrent challenge is incorporating and visualizing point defects—like vacancies or substitutions—into periodic crystal models. These small changes can drastically affect the physical and…

When communicating molecular mechanisms, clarity matters. Whether for educational content, journal illustrations, or presentations, effectively showing what appears—and more importantly, what disappears—can help molecular modelers deliver their message without visual noise. If you’ve ever needed to hide specific molecules or…

When modeling molecules, accurate and up-to-date measurements are critical. Whether you’re working on distances, angles, or torsions, being able to capture and revisit your measurements — and share them clearly with colleagues — can save time and reduce ambiguity in…