Author: OneAngstrom

When preparing scientific presentations or videos, one of the most common frustrations for molecular modelers is illustrating how components of a complex biomolecular system separate or disengage—without adding unnecessary clutter or manually repositioning dozens of atoms or structures. This is…

One of the common challenges in molecular modeling is keeping track of specific parts of a complex system during simulations or animations. For instance, you may want to closely follow an active site in a protein, or a ligand as…

One of the most common and time-consuming tasks in molecular modeling is selecting subsets of atoms and tweaking their properties. Whether you’re preparing input structures, scripting transformations, or just exploring molecular shapes, doing this atom-by-atom can quickly become inefficient and…

In medicinal chemistry and molecular modeling, exploring molecular variations through analog generation is often a key step in optimizing compounds. But modifying molecules atom-by-atom, especially when dealing with a high number of analogs, can be slow and error-prone if done…

Generating reliable membrane-protein systems can quickly become a time-consuming task for molecular modelers. Between aligning proteins, setting up lipid orientations, tuning margins, and ensuring correct placement, a lot can go wrong. Fortunately, Molecular Box Builder in SAMSON simplifies the process…

If you’ve ever docked a ligand into a protein structure and wondered why the results weren’t quite what you expected, you’re not alone. One of the most frequent—and easily overlooked—issues in molecular docking is whether to perform protein structure preparation…

When working with protein systems, especially in coarse-grained (CG) simulations using force fields like MARTINI, it’s common to use multiple copies of a protein within a simulation box. But as many molecular modelers have experienced, creating replicas can easily lead…

For molecular modelers working on protein-ligand complexes, deciphering complex interaction patterns can be challenging, especially when navigating dense 3D environments. Identifying hydrogen bonds, hydrophobic contacts, and clashes visually in 3D often requires substantial effort—and sometimes even multiple tools. The Interaction…

When creating molecular animations, one common frustration is the unintended shifting of the camera viewpoint between frames. You might spend time meticulously orienting your view—zooming, rotating, and positioning molecules just right—only to discover that later frames don’t retain your chosen…

For molecular modelers working with carbon nanostructures, creating accurate models of carbon nanotubes (CNTs) can be a time-consuming task—especially when aiming to simulate or analyze multi-walled configurations. Whether you’re preparing for a simulation, visualizing a nanostructure for publication, or testing…