OneAngstrom – Page 229

Adding a Lipid Bilayer Around a Protein Without Clashes

One of the most common scenarios in molecular modeling is embedding a membrane protein into a lipid bilayer. While it sounds straightforward, anyone who has tried to manually position hundreds of lipids around a protein knows this can be a…

Controlling Perspectives with Camera Animations in SAMSON

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One challenge that comes up again and again in molecular modeling is how to clearly communicate structural insights to others. Whether you’re preparing a presentation, building a tutorial, or creating a publication-quality video, controlling the camera’s motion is essential. This…

Building Your First Custom Tool in SAMSON: A Starting Point for Developers

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Molecular modeling often requires performing highly specialized simulations, visualizations, or data workflows—tasks that might not be fully covered by existing tools. This gap frequently leads scientists and developers to create their own scripts or pipelines. But wouldn’t it be more…

Let Your Molecules Fade Away: Creating Disappearing Effects in SAMSON

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Visual presentation is a critical aspect of molecular modeling, especially when preparing demonstrations, tutorials, or research presentations. One common challenge faced by molecular modelers is how to control the visibility of atoms, molecules, or annotations in a smooth and convincing…

How to Control the Visibility of Backbones in SAMSON with Attribute Flags

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When building and analyzing molecular systems in SAMSON, one often needs to focus on specific structural components. For many research projects, this means hiding or revealing backbone structures to reduce visual clutter or highlight important elements. This seemingly simple action…

Making Atoms Appear One by One: A Useful Trick for Molecular Animations

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One recurring challenge in molecular modeling is how to build better visual narratives when presenting mechanisms, processes, or molecular structures. Whether you’re preparing for a lecture, scientific presentation, or simply want to communicate structural insight more clearly, animated transitions help…

Animating Molecular Motion without Code: A Visual Approach Using Move Atoms in SAMSON

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When communicating complex molecular behavior, nothing beats a well-crafted animation. Whether you’re illustrating ligand dynamics, protein flexibility, or simply aligning datasets for a presentation, conveying atomic motion in an intuitive way matters. Many molecular modelers, however, still rely on tedious…

How to Build a Multi-Walled Carbon Nanotube in Under a Minute

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Creating accurate carbon nanotube (CNT) models can be time-consuming and technically complex, especially when trying to design concentric multi-walled structures. Whether you’re working in nanotechnology, molecular design, or materials science, generating realistic CNT models fast is essential for iterative research…

Don’t Let Your Simulations Steal Your CPU: Tuning GROMACS Performance in SAMSON

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Running molecular dynamics simulations with GROMACS can be computationally demanding, especially on your personal machine. If you’ve ever noticed your entire system getting sluggish while simulations run, you’re not alone. GROMACS is designed to use your machine efficiently, but when…

Quickly Filter Large Molecular Models by Atom Count in SAMSON

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Working with large datasets in molecular modeling often means dealing with hundreds or even thousands of structures. Filtering through these models to identify only those relevant to a specific task—such as those with a manageable number of atoms—can be tedious.…