Molecular modelers often face a common challenge when presenting their work: how to visually communicate the dynamic process of molecular assembly or structural evolution across frames. Whether you’re demonstrating the progressive construction of a biomolecular complex or tracking which atoms…

When analyzing or designing protein structures, molecular modelers often encounter the challenge of working with incomplete biological assemblies. PDB files offer a rich source of structural data, but this data can be encoded in multiple ways — complicating the reconstruction…

When building molecular models, clarity is everything. Whether you’re preparing figures for a publication or trying to better understand your system, labels play a crucial role in making data stand out. But what happens when your labels overlap with atoms,…

Working with GROMACS simulations often requires a deeper level of system customization—especially when analyzing specific molecular interactions or controlling particular subsets. If you’re looking to pull a specific group of atoms or analyze a charged residue cluster, you probably need…

When working on complex molecular systems, sometimes you need to refine only a specific part of a molecule—perhaps a side chain in a protein or a distorted fragment—without altering the rest of the structure. Fully minimizing the entire system can…

When crafting molecular animations, a common challenge faced by modelers is how to emphasize key events—such as the binding of a ligand or the disappearance of a residue—without overwhelming the viewer with continuous motion. Sometimes, less is more. The Flash…