Author: OneAngstrom

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…

As a molecular modeler, it’s common to examine distances, angles, or torsions between atoms—but it’s equally common to lose track of those measurements when switching views or making a new selection. If you’ve ever thought, “Where did my previous distance…

Molecular modelers often work with complex structures containing thousands of atoms, residues, ligands, and other node types. Selecting the right subset of these nodes precisely and efficiently can be a challenge, especially during structure analysis, preparing simulations, or performing molecular…

Many molecular modelers rely on GROMACS to simulate molecular dynamics because of its flexibility, performance, and open-source nature. While integrative platforms like SAMSON offer out-of-the-box integration with GROMACS, a common need arises: what if your project requires a specific version…

When presenting complex molecular mechanisms or structural transitions, molecular modelers often encounter a recurring problem: how to clearly communicate spatial changes without overwhelming their audience. Whether your goal is to demonstrate a protein’s binding interface or visually highlight subunit relationships,…