Author: OneAngstrom

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…

Molecular modeling can be both fascinating and overwhelming—especially when you’re just getting started. You’ve launched SAMSON, the integrative molecular design platform, and dozens of menus, toolbars, and viewers greet you. Now what? One of the most common issues faced by…

If you often find yourself applying the same sequence of visualizations when working on molecular systems—setting colors, choosing representations, focusing on ligands—you are not alone. Consistency in visualization is key for insights, collaboration, and publication. But endlessly repeating the same…

Collaborating on molecular projects often involves more than just sharing a molecular structure. From scripts and input files to figures and related data, managing and organizing all the assets linked to a research project can be a challenge—especially when working…