OneAngstrom – Page 322

Precise Molecular Alignment in SAMSON Without Scripting

Aligning molecular structures in 3D space is a common task in molecular modeling workflows. Whether you’re preparing a system for analysis, visualizing structures together, or setting up simulations, the ability to quickly and accurately align molecules along reference axes or…

Efficiently Setting Initial Conformations for Batch Simulations in SAMSON

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When preparing molecular dynamics simulations, researchers often work with multiple starting conformations of the same system. This is especially common in studies involving ligand binding, protein flexibility, or comparative dynamics. However, managing and configuring these conformations for batch simulations can…

Quickly Locate and Manage Hidden Molecular Visual Models in SAMSON

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When working with complex molecular scenes in SAMSON, it’s common to end up with dozens, even hundreds of visual model nodes representing atoms, bonds, surfaces, isosurfaces, meshes, and more. As the project grows, things can become visually overwhelming — or,…

Avoid Common Mistakes When Setting Up MARTINI Force Fields in Coarse-Grained Simulations

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One of the challenges molecular modelers often face when working with coarse-grained (CG) molecular dynamics simulations is properly setting up force fields—particularly for MARTINI-based systems. A mismatch in force field parameters can lead to hours of debugging, poor system stability,…

How to Select Atoms with Precision in SAMSON Using Mathematical Expressions

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When working with large molecular structures, molecular modelers often face the challenge of isolating specific atoms for inspection or modification. Manually selecting these atoms can be tedious and error-prone—especially in systems with thousands or millions of atoms like biomolecular complexes,…

Quickly Filter Visible Molecular Backbones in SAMSON

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When working on large and complex molecular systems, it’s easy to get overwhelmed by the sheer number of components displayed in the viewport. You might find yourself hunting for just the visible backbones of a protein, or trying to select…

Quickly Filter File Nodes in SAMSON with These 3 Attributes

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When working on complex molecular models, especially in large systems with multiple datasets, managing and filtering different nodes in your project becomes crucial. Many users of the SAMSON molecular design platform need a fast way to query and act on…

Making Your Molecular Projects Portable with File Embedding in SAMSON

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Working with molecular models often means juggling several types of files: structures, scripts, datasets, documents, and even code. Anyone who has ever transferred a molecular project from one machine to another—or tried to share it with a collaborator—knows how easy…

Creating Attention-Grabbing Molecular Transitions with Flash Animation in SAMSON

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When creating molecular animations, effectively guiding your viewer’s attention is a major challenge. Whether you’re preparing an educational video, a presentation for colleagues, or a publication-grade animation, cleanly controlling when molecular systems appear and disappear can make your message clearer.…

Visualizing Ligand Motions: Exporting Unbinding Pathways from SAMSON

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Molecular modelers often spend a considerable amount of time simulating ligand unbinding pathways in protein-ligand systems. However, after the hard work of generating results, exporting and visualizing the actual ligand motions can still be confusing or time-consuming. If you’ve been…