Author: OneAngstrom

One of the constant challenges faced by molecular modelers is simplifying complex molecular scenes for presentations or animations. Whether it’s to highlight a reaction site, declutter overlapping strands, or direct attention to a specific structure, controlling visibility is a key…

Aligning molecular structures may sound simple, but anyone working at the atomic level knows that precision matters—whether you’re comparing docking poses, preparing figures, or building assemblies. If you’ve ever wrestled with rotating, translating, and centering molecules manually, this post is…

When exploring new molecules in drug discovery or materials science, seeing the molecule in 3D isn’t a luxury—it’s a necessity. However, for many molecular modelers, converting a generated 2D molecular structure (e.g., from a SMILES code) into its 3D counterpart…

When setting up a molecular dynamics simulation involving pulling or restraining specific molecular parts, having precise control over which atoms belong to which group is crucial. This is especially important in center-of-mass (COM) pulling simulations where specifying exactly which atoms…

Molecular modelers often juggle multiple tasks: building structures, transforming geometries, applying selection tools, and more. Every operation requires precision, and switching gears between different tools should be seamless. That’s where the editor system in SAMSON comes in. Understanding how editors…

Have you ever needed to visualize how atoms move over time during your molecular animation? Whether you’re showcasing a docking process, simulating molecular dynamics, or illustrating a mechanism of action, a common challenge is to record and later export clear…

Validating and refining protein structures often involves ensuring that backbone conformations fall within energetically favorable regions. When dihedral angles (φ and ψ) are off, a residue may adopt a strained conformation that can compromise structural stability or the results of…

When working with large biological assemblies—such as viral capsids, multimeric protein complexes, or nanostructures—symmetry can be both a friend and a challenge. Detecting symmetry reduces computational load and helps identify biologically meaningful patterns. But what happens when multiple symmetry groups…