OneAngstrom – Page 318

Why Molecular Modelers Should Start Using Multiple Cameras

When designing complex molecular systems, getting the right perspective can significantly enhance both understanding and productivity. One common source of friction in many workflows is the constant need to rotate, zoom, and reposition your view as you analyze or present…

Quickly identify specific bond types in your molecular models

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When modeling molecular systems, it’s often essential to distinguish between different types of chemical bonds. For instance, detecting all aromatic or amide bonds in a structure can give valuable insight into reactivity, structural stability, or conformational preferences. However, doing this…

Making Molecules Rock: A Simple Way to Add Movement to Your Models

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Have you ever wanted to bring your molecular models to life with more than just static visuals? For many molecular modelers, especially those preparing educational content or scientific presentations, adding subtle yet meaningful animations can help convey structure, function, and…

Quickly Select Backbone Groups with Specific Atomic Composition in SAMSON

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In molecular modeling projects involving large biomolecular systems, tasks such as identifying backbone structural groups with specific atomic counts or charge characteristics can be time-consuming. Whether you’re preparing a dataset, analyzing systems, or building coarse-grained models, manually filtering and inspecting…

When and Why You Should Minimize Ligands Before Docking

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Anyone working on molecular docking knows that preparing ligands properly can make or break the resulting poses. But a common question that arises is: should I minimize my ligands before docking? If you’ve faced odd docking poses or inconsistent scoring,…

Showing Disappearance in Molecular Models: A Closer Look at the ‘Conceal Atoms’ Animation

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When presenting molecular models, transitions can be just as important as the models themselves. Animating what appears or disappears — and how — can help deliver clearer, more focused presentations. One common challenge in dynamic molecular visualization is how to…

Orbit Camera: A Simple Way to Get Stunning Molecular Visuals

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Creating visually engaging presentations of molecular structures can be challenging, especially when trying to communicate concepts in a dynamic and appealing way. Static images often fail to capture the complexity and spatial relationships between atoms and molecules. This is where…

Bringing Your Molecular Tools into SAMSON

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Many molecular modelers face a familiar challenge: you’ve already developed tools or use third-party software for simulations, docking, or visualization — but managing interoperability becomes time-consuming and error-prone. If you’re switching between tools or manually parsing results across platforms, you’re…

Simplifying Ligand Separation: Using the Undock Animation in SAMSON

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Visualizing molecular motion is crucial when designing presentations or exploring structural hypotheses in molecular modeling. One of the challenges often faced by modelers is effectively communicating the concept of molecular dissociation — for example, when an inhibitor unbinds from a…

Tracking Ligand Motion: Visualizing Center-of-Mass Paths in Molecular Simulations

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When working with molecular dynamics simulations, one common challenge is efficiently interpreting the spatial motion of critical molecular components like ligands. Particularly during processes like ligand unbinding, domain shifts, or diffusion, it’s easy to get lost in a sea of…