Author: OneAngstrom

When working with complex macromolecules, pinpointing specific residues in a structure isn’t always easy. As the number of chains and atoms increases in your 3D molecular model, the challenge grows: which residue is where, and how do different regions of…

Sometimes, molecular modeling isn’t just about data—it’s about telling a clear, visual story. Whether you’re preparing a scientific presentation, a student tutorial, or a molecular animation for a publication, you may face this common problem: how to make some molecular…

During molecular simulations, it’s not uncommon to lose track of the structural elements you’re most interested in. You try to follow a subunit or a specific site, but as the animation plays out, your perspective shifts—even when you wish it…

For many molecular modelers, producing high-quality visualizations from complex molecular systems is a time-consuming task. Whether for presentations, publications, or simply to better understand molecular structures, styling a model typically involves many steps — selecting components, choosing representations, applying color…

When modeling biomolecular systems at a coarse-grained (CG) level using the MARTINI force field, one common situation arises: scientists often want to simulate *multiple replicas of the same protein*, such as in crowded environments or assembly studies. However, preparing such…

One of the recurring challenges in protein modeling is refining structures to ensure that all residues adopt energetically favorable conformations. Residues with dihedral angles in disallowed regions can introduce errors in simulations or reduce structural quality in homology models. But…

When preparing animations of molecular systems, one of the common challenges modelers face is managing what’s visible—either momentarily or throughout a sequence. Sometimes, showing specific elements of a simulation at just the right moment is crucial to helping others understand…

Filtering and analyzing molecular structures can become time-consuming when dealing with large assemblies. For computational chemists, structural biologists, or anyone routinely working with complex molecular data, pinpointing specific residues, bonds, chains, or functional groups quickly is essential—but often tedious. Fortunately,…

Many molecular modelers work with simulation setups that are too large or too computationally expensive to be run comfortably on their local machines. While GROMACS is efficient, setting up a local high-performance computing environment—and maintaining it—is not ideal for many…