One of the common pain points in molecular modeling is managing and synchronizing selections between 3D structures and the sequence data they represent. As structures become more complex with multiple chains and intricate residue interactions, staying organized while moving between…

If you’ve ever created a molecular animation and wished for more control over how the camera moves through your system, you’re not alone. Many molecular modelers run into limitations when trying to zoom in smoothly or direct attention to a…

Visualizing molecular structures is fundamental to communicating and understanding complex molecular behavior. However, making static 3D models engaging and clear is not always easy. Molecular modelers, educators, and researchers alike know the struggle: how do you highlight a particular group…

When working with complex biological assemblies—viral capsids, oligomeric proteins, or large multimeric structures—leveraging their symmetry can significantly reduce computational costs, simplify analysis, and enhance structural interpretation. But what happens when multiple symmetry groups are detected for a single structure? In…

When preparing systems for molecular simulations using coarse-grained (CG) models, researchers often face a common hurdle: how to efficiently replicate molecular structures—such as proteins—multiple times with unique chain and residue identifiers, all while keeping the system organized for tools like…

Molecular animations are a central part of communicating molecular behavior, structure, and dynamics. Whether you’re preparing a scientific presentation, an educational video, or simply making your simulations more engaging, having clear visual tools to illustrate your data can help others…

Before launching molecular dynamics simulations, there is a critical preprocessing step that often gets overlooked: energy minimization. This step is key to ensuring that your molecular system is stable and realistic enough to proceed with confidence. But why is it…

Following atomic motion during a simulation can reveal a great deal about molecular mechanisms, such as how a ligand unbinds from a protein or how internal domains move collectively. Yet, for molecular modelers, focusing on individual atom trajectories can be…