OneAngstrom – Page 23

Tips for Defining an Efficient Sampling Box for Ligand Unbinding Pathways

Finding ligand unbinding pathways through protein tunnels is a common need in molecular modeling. But did you know that the way you define the sampling region can significantly influence the results? In this blog post, we focus on a critical…

Registering Your Own Monomers in SAMSON’s Polymer Builder

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If you’re working with custom polymers, one of the most repetitive (and error-prone) steps in your workflow might be building complex chains from fragments you designed. Whether you’re researching synthetic polymers or developing molecular scaffolds for prediction models, you likely…

Speed Up Your Molecular Visualization Workflow with Visual Presets

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Molecular modeling often requires combining clarity with aesthetic quality. When working with complex biomolecular systems, it can be time-consuming to apply multiple visual layers manually — ribbons for secondary structures, sticks for ligands, van der Waals spheres for ions, color…

An Easier Way to Present Molecules: Orbit Camera Animation in SAMSON

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Creating compelling molecular presentations can be time-consuming, especially when manually adjusting your camera to depict structures from different angles. If you’ve ever tried to record a fly-around of a protein complex or a crystal structure, you know how hard it…

Where to Find Specialized Tools for Molecular Modeling in SAMSON

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For many molecular modelers, one persistent challenge is finding the right specialized tool for a specific task. Whether you’re visualizing electron densities, editing complex structures, or running cloud simulations, the core installation of a modeling platform might not offer the…

Quickly Identify Selected Node Groups While Modeling Molecules

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When working with large molecular systems, it’s common to organize atoms and molecules into node groups in SAMSON, the integrative platform for molecular modeling. These groups help you manage complex scenes—from protein-ligand interactions to nanoscale assemblies. But once the complexity…

Tired of Hunting for Atom Properties? Use This Quick Filter Trick Instead.

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When working on complex molecular structures, it’s easy to feel overwhelmed by the number of properties associated with each atom. Whether you’re adjusting atom positions during molecular modeling or inspecting attributes to verify structural consistency, sifting through all the information…

Easily Switch Between Molecular Selections with Quick Groups in SAMSON

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Working on large or complex molecular systems often involves switching between several regions of interest — ligands, receptors, water molecules, cofactors, etc. Repeating selection steps every time can quickly become tedious and error-prone. Quick Groups in SAMSON address this pain…

Quickly Select Chains by Properties in SAMSON Using the NSL

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Working with molecular models that include multiple chains can often feel overwhelming—especially if you’re trying to select or isolate specific chains based on unique criteria. Whether you’re preparing a simulation, analyzing a structure, or simply cleaning up a model, being…

Tracing Molecular Motion with Center-of-Mass Pathlines

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One of the common challenges for molecular modelers is understanding how molecular components move during simulations. Whether you’re tracking a ligand unbinding from its binding pocket or studying large conformational transitions in proteins, getting a clear view of motion across…