OneAngstrom – Page 208

A Precise Spin: Rotating Atom Groups in SAMSON for Better Molecular Presentations

When preparing molecular animations and presentations, many researchers and students struggle to create clear and engaging visual sequences that effectively communicate structural features and motions. A recurring challenge is how to rotate parts of a molecular system smoothly and precisely,…

How to Control Molecular Fragment Orientation in SAMSON

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When building molecular structures, one of the recurring challenges for molecular modelers is precisely controlling how fragments connect — especially when assembling complex molecules. Poorly oriented fragments can lead to atomic clashes, unrealistic geometries, or tedious manual corrections. Fortunately, SAMSON…

Tuning SAMSON’s Dark Mode for Long Modeling Sessions

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Long hours in front of glowing molecules can take their toll. If you’re a molecular modeler working late into the night, or simply prefer a more comfortable visual environment, SAMSON’s Dark mode preferences may help reduce eye strain and give…

Making Molecules Appear Smoothly in Your Presentations

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When preparing molecular animations, every detail can affect clarity and impact. If you’ve ever wanted to make a model gradually appear—rather than just pop into view—the Appear animation in SAMSON can help you do just that. This subtle visual effect…

Preview and Generate Protein Symmetry Mates Interactively

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When working with proteins in PDB format, one of the recurring challenges is understanding how a structure fits into its larger biological context. Many deposition files contain only an asymmetric unit—just a fragment of the full biological assembly. This often…

Visualizing the SARS-CoV-2 Spike’s Opening in 3D: A Practical Guide for Molecular Modelers

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Understanding molecular motion is crucial in structural biology and molecular design, especially when studying protein-ligand interactions or conformational transitions. But modeling flexible structures like the SARS-CoV-2 spike protein can be technically challenging and time-consuming. Knowing how to simulate such motions…

Quickly Filter Visible Labels in Molecular Models Using SAMSON

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When working with complex molecular systems in SAMSON, label nodes play a key role in annotating structures, highlighting specific data, and guiding collaborators. However, once your scene becomes crowded, it can be hard to keep track of which labels are…

Stop Wasting Clicks: Filter Render Presets in SAMSON with a Few Keystrokes

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A common pain for molecular modelers and visualizers is efficiently managing complex scenes with many render presets. When dealing with multiple visual styles—cartoon, licorice, surface, and more—it’s easy to lose track of your custom presets, especially in large systems. You…

Need to track how atoms move? Here’s a way to record their path during animations.

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When preparing molecular presentations or designing animations of molecular mechanisms, one recurring challenge for modelers is tracking how atoms move over time. Whether you’re simulating a docking event, assembling a complex, or simply visualizing structural changes, keeping a clear record…

Visualizing Molecular Motions Without Running Full Simulations

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Computing conformational changes in large macromolecular systems is often time-consuming and computationally intensive. What if you need a representative trajectory between two known structures but can’t afford to run costly molecular dynamics simulations? For molecular modelers looking to visualize and…