OneAngstrom – Page 133

A Clearer View of Molecules: How Ambient Occlusion Enhances Depth Perception

One of the most common challenges in molecular modeling and visualization is understanding the spatial relationships within complex structures. When looking at dense molecular systems, it can be hard to tell which atoms are deep inside a pocket and which…

Bring molecular models to life with the Pulse animation

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When creating molecular animations, it’s often challenging to make transitions visually intuitive. If you’re showing a model appear and disappear during a presentation or video, a harsh on–off switch can make the experience jarring. This is particularly relevant for molecular…

Publishing Extensions on SAMSON: What You Need to Know

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For researchers and developers creating custom tools for molecular design or simulations, one common roadblock is: how to share your software with collaborators or the broader community? Whether it’s an app that wraps an existing simulation, an importer for specialized…

Managing Visibility in Molecular Models: A Quick Guide Using NSL

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When you’re working on complex molecular systems, there’s often a point where your visualization gets cluttered. Maybe you’re trying to focus on specific interactions while eliminating distracting nodes. Or perhaps you’re preparing a figure for a publication and need only…

Simplifying Molecular Visualization with the Orbit Camera in SAMSON

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Creating compelling molecular animations is a crucial part of science communication and insightful model analysis. However, producing smooth and precise camera movements that gracefully orbit around a molecule is often a technical challenge. This becomes especially important when preparing videos…

Avoid Topology Errors: Renumbering Chains and Residues Before Martinizing

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When generating coarse-grained (CG) models for molecular simulations using Martinize2 in SAMSON, one common issue arises when your system contains multiple chains or replicas: overlapping residue and chain identifiers. This can lead to errors during topology generation, especially in .top…

Saving and Restoring Molecular Conformations with Ease

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When exploring molecular systems, many researchers face the challenge of navigating between different conformations—a particular geometric state of a molecule. Whether tweaking a ligand’s side chain or optimizing a nanotube’s structure, saving stable intermediate positions can be surprisingly valuable. If…

Easily Select Molecular Groups by Atom Counts in SAMSON

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Working with complex molecular systems often means working with large numbers of atoms and intricate structural details. Whether you’re preparing a structure for simulation, analyzing molecular interactions, or customizing visualizations, you may often ask yourself: “How can I quickly select…

Customizing Molecular Dynamics Parameters in SAMSON Without the Headache

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Choosing the right set of molecular dynamics (MD) parameters can make a significant difference in the fidelity and outcome of your simulations. But for many molecular modelers, manually editing and keeping track of .mdp files can be error-prone and time-consuming—especially…

Comparing Symmetry Groups: How to Pick the Right One for Your Molecular Assembly

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When studying large protein complexes or viral capsids, symmetry isn’t just beautiful—it’s practical. Detecting and analyzing symmetry in your biological assemblies can dramatically reduce simulation costs and improve the quality of your models. But what happens when your structure doesn’t…