OneAngstrom – Page 72

Quickly Find the Render Presets You Need with NSL Attributes

Working on complex molecular scenes often means dealing with many different visualization styles. Whether you’re organizing a biomolecular assembly or preparing figures for publication, managing and filtering render presets in SAMSON can get a bit tricky — unless you know…

Frustrated by Ambiguous Node Selections? Here’s How NSL Can Help

OneAngstrom

Anyone who regularly models molecular systems knows that managing atom, residue, or structural selections can quickly become a tedious and error-prone task. Whether you’re dealing with large protein complexes, ligands, or custom structural groups, clicking through endless menus or misclicking…

Choosing the Right Unit Cell Shape Can Save You 29% CPU Time

OneAngstrom

When setting up molecular dynamics simulations, especially with approximately spherical molecules in solution, most modelers focus heavily on force fields and solvent types. Yet, there’s an often-overlooked choice that can bring significant performance benefits: the shape of the unit cell…

Selecting Molecular Backbones by Atom Count: A Quick Guide

OneAngstrom

A common challenge in molecular modeling is quickly isolating parts of a model based on structural complexity. For instance, you might want to find backbones with a specific number of atoms or carbon, hydrogen, or oxygen content—without visually scanning through…

From Molecule to Insight: Replacing Functional Groups with SMILES Manager

OneAngstrom

Exploring the effects of small chemical modifications on a lead compound is a daily task for many molecular modelers, particularly when optimizing a series of analogs for desirable properties like potency, selectivity, or ADMET characteristics. However, this form of structure-activity…

Making Atoms Appear: A Practical Guide to the Show Animation in SAMSON

OneAngstrom

Molecular modelers often face the challenge of presenting their work in a clear and intuitive manner. When creating animations of molecular systems—whether for presentations, publications, or teaching—controlling *when* specific atoms or groups become visible is essential. Flickering atoms or unclear…

Creating Molecular Animations and Presentations in SAMSON: A Practical Introduction

OneAngstrom

Animations are a powerful way for molecular scientists to communicate complex structures and phenomena clearly. Whether you’re teaching molecular docking, showcasing a simulation, or presenting a structural transformation, effective animations save time and help others understand your work faster. But…

Making Molecular Assemblies Clearer with the Assemble Animation in SAMSON

OneAngstrom

Creating effective visual presentations of molecular systems can be time-consuming. One common challenge molecular modelers face is clearly showing how individual components of a complex structure come together. Whether preparing figures for a paper or animations for a presentation, clearly…

Tracking Molecular Measurements Permanently with Labels in SAMSON

OneAngstrom

When modeling molecular systems, a recurring frustration among researchers is having to remeasure distances, angles, or torsions each time the system changes or is reopened. Whether you’re analyzing bond lengths after a minimization or monitoring torsion angles in a conformational…

A More Intuitive Way to Fix Outliers in Protein Models

OneAngstrom

Refining protein structures can be inefficient when outlier residues fall outside allowed conformations in a Ramachandran plot. If you’ve ever opened a homology model or experimental structure only to see white dots far from the safe yellow zones, you know…