OneAngstrom – Page 140

Editing Bonds with Physics: Interactive Modeling with IM-UFF in SAMSON

When working with molecular models, one frequent challenge scientists face is modifying structures without breaking the simulation pipeline. Whether you want to prototype a new molecule, adjust a ligand, or refine a complex configuration, editing molecular bonds can easily disrupt…

How to filter labels in complex molecular scenes without getting lost

OneAngstrom

When working with detailed molecular models, annotations like labels are key to keeping your scene understandable. But as your system grows, so does the visual clutter. If you’ve ever struggled to selectively show, hide, or search for label nodes in…

Simplifying Molecular Presentations with the Hide Animation in SAMSON

OneAngstrom

When preparing visual presentations of molecular systems, especially for education, publications, or collaboration, one recurring challenge is controlling the visibility of elements over time. As systems grow in complexity, parts of the model may need to be temporarily removed from…

Color Schemes in Molecular Design: A Practical Guide to Clarity in SAMSON

OneAngstrom

One of the key challenges that molecular modelers face is keeping large biomolecular systems readable and informative during visualization. Whether presenting to collaborators or simply making sense of complex macromolecular structures themselves, researchers often struggle with visual clutter, indistinct representations,…

Quickly Find Atoms, Molecules, and Chains in Complex Models

OneAngstrom

Working with large molecular models can be overwhelming. Whether you’re analyzing a multi-chain protein, a coarse-grained system, or a ligand-binding ensemble, the key to productivity is being able to quickly find what you’re looking for. This is where the Node…

When and How to Minimize Ligands Before Docking in AutoDock Vina Extended

OneAngstrom

Minimizing ligands before docking is a step that’s often undervalued, yet crucial for improving docking performance and reliability. If you’ve ever encountered unexpected artifacts in your docking poses, especially when using a ligand library, chances are the root cause was…

Saving Just the Atoms You Need: Exporting Subsets Along Molecular Paths

OneAngstrom

When studying complex molecular pathways—like ligand unbinding, conformational transitions, or induced fit mechanisms—molecular modelers often need to extract atomic trajectories along specific paths. But exporting an entire structure is often overkill. What if you’re only interested in a ligand, a…

A Simple Way to Visualize Ligand Unbinding Paths in Molecular Simulations

OneAngstrom

Tracking the motion of ligands during molecular simulations is often essential to understanding binding and unbinding mechanisms, but extracting meaningful insights from raw trajectory data can be time-consuming or visually unclear. If you’ve ever searched for a clear way to…

Progressively Hiding Atoms in Molecular Animations Without Changing Transparency

OneAngstrom

One of the recurring challenges in molecular modeling and visual communication is directing attention to specific parts of a molecule. Whether you’re preparing a presentation, creating a tutorial, or crafting a demo for students, hiding parts of a structure needs…

Transforming Static Structures into Dynamic Insights: Visualizing Protein Transition Paths with ARAP

OneAngstrom

One recurring challenge in structural biology and molecular modeling is how to study conformational changes between two known protein structures. Whether you’re investigating molecular mechanisms, setting up umbrella sampling simulations, or simply trying to better understand flexibility in biomolecules, capturing…