Sharing reproducible, working molecular models with others—students, colleagues, or collaborators—can be a challenge when your workflow depends on multiple scripts, data files, or third-party tools. How often have you sent a Python script over email or GitHub, only to have…

When working with molecular models, it’s often crucial to examine which atoms or residues are near a specific site of interest. Whether you’re studying binding pockets, analyzing molecular interactions, or inspecting local environments, being able to precisely select nearby nodes…

When presenting molecular systems, especially in animations, clarity of focus can make all the difference. Whether you’re creating a visual explanation for a complex biomolecular interaction or preparing insightful imagery for publication or teaching, the ability to zoom smoothly into…

For molecular modelers juggling different tools, scripts, and data files, maintaining consistency, reproducibility, and portability across projects often becomes a challenge. Whether you’re working on protein-ligand docking, simulating reaction mechanisms, or analyzing trajectories, your work usually relies on custom scripts,…

When building or modifying molecular models, structure alignment may seem like a small step—but it can have a big impact. Misaligned atoms or molecules can lead to misleading visuals, unnecessary complexity during simulation, or trouble when exporting for publications or…

One of the key challenges in molecular modeling is ensuring that the geometry of your structure is physically realistic. Whether you’re assembling custom molecules or importing existing ones, minimizing structural strain is essential to avoid artificially high energies and forces.…

When analyzing molecular simulations, one of the recurring challenges is maintaining visual focus on a specific group of atoms during animation. Whether you’re tracking how a ligand moves inside a binding pocket or examining the structural flexibility of a protein…

If you've ever tried analyzing or running custom simulations in GROMACS, you've probably faced this: you need a specific group of atoms that isn’t covered by default index groups like Protein, Water, or Ion. Maybe you want to pull on…