Author: OneAngstrom

When working with complex biomolecular systems, navigating 3D structures to select specific residues can be time-consuming and error-prone. Whether you’re preparing a simulation, designing a mutation, or analyzing a structural motif, efficient residue selection matters. Fortunately, SAMSON offers a synchronized…

When manipulating molecular structures, it’s easy to make small changes that have big consequences—like accidentally moving an atom… or several. If you’ve ever found yourself wondering how to precisely adjust or revert attributes of different parts of your molecular model,…

When sharing molecular models—whether it’s for a presentation, a publication, or simply collaboration—clarity and consistency matter a lot. Screenshots taken from visualization software are often inconsistent in size, format, or even visibility due to cluttered interfaces or unsuitable backgrounds. If…

For many molecular modelers, selecting specific parts of large molecular structures—residues in a chain, atoms in a binding site, or side chains near a ligand—can be a recurring bottleneck. Traditional selection involves manually clicking through models or crafting complex queries…

Designing molecular systems from scratch can be time-consuming. For molecular modelers, every minute spent re-assembling common fragments like benzene rings or amino acids is a minute not spent on optimization, analysis, or simulation. If you’ve ever thought “I’m sure I’ve…

When working on molecular presentations or dynamic studies in SAMSON, it’s common to encounter an unexpected shift in the camera view between animation frames. You may have carefully adjusted the orientation of a complex biomolecular system, only to find the…

When working on complex molecular models, it’s easy to feel overwhelmed by the tools available. From deforming structures to generating nanotubes or selecting regions of a model, the number of functionalities can pile up quickly in a molecular modeling interface.…

One of the most common pitfalls in molecular dynamics simulations—particularly involving pulling experiments—is improper box sizing in the direction of pulling. If your molecule gets too close to the edge of the simulation box, periodic boundary conditions can create unwanted…

Communicating molecular insights often requires more than just static images. When presenting dynamic processes like conformational changes, reaction mechanisms, or structural rearrangements, fine control over visibility can convey meaning more effectively. A common issue for molecular modelers is how to…