If you’ve ever created a molecular animation and felt frustrated by the sudden appearance or disappearance of molecular structures, you’re not alone. Many molecular modelers want to smoothly introduce structures over time, especially when visualizing things like conformational changes, ligand…

When creating molecular animations or presentations, clarity and continuity matter. It’s easy to overlook how changes in the camera view can disrupt the flow of a molecular video or compromise the viewer’s understanding. Have you ever looked back at an…

The frustration is familiar to many molecular modelers: you’ve built or downloaded a molecular structure, set everything up for a simulation, only to find out that your model contains steric clashes or non-ideal geometries that cause your simulation to crash…

Molecular modeling workflows often involve numerous delicate operations—adding atoms, adjusting geometries, rerunning simulations, and more. But what happens when one step goes wrong or you accidentally overwrite something important? The frustration of not being able to revert to the previous…

Choosing the right molecular visualization style can be unexpectedly time-consuming. From setting up color schemes to applying visual representations, it’s easy to get lost in the details — or worse, struggle to reproduce previous results. If you need a quick…

When modeling molecular transitions, setting up your system properly is as important as the results you want to obtain. Protein structures from the Protein Data Bank (PDB) are often not ready to be used directly in simulations or path interpolations.…

For many molecular modelers, getting started with new software can be a time-consuming process. Advanced platforms often come with complex interfaces, and even experienced users can find themselves spending hours trying to accomplish what should be a simple task. Wouldn’t…

When working with molecular simulations, especially those that rely on force fields like the Universal Force Field (UFF), one frequent pain point is correctly setting up a molecular system for simulation. A common obstacle arises during bond perception—how bonds, bond…

When working with complex molecular models, one of the key challenges is filtering specific parts of a structure — like selecting only side chains, residues from a certain range, or atoms bonded to specific groups. If you’ve ever found yourself…