SAMSON Blog – Page 72

From Docked to Undocked: Visualizing Molecular Detachment with Ease

If you’ve ever tried to explain or visualize how a ligand detaches from a receptor—or how components of a molecular system move apart during a simulation—you’ve probably encountered this common challenge: how do you create a clear, visually engaging animation…

Quickly Identifying Molecular Folders With Specific Structures in SAMSON

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Modeling complex molecular systems often involves navigating through large, layered hierarchies of folders in your design environment. If you’ve ever found yourself digging through countless folders in SAMSON trying to locate a structure with precisely 100 to 200 atoms or…

A Better Way to Animate Atoms: Avoid Rebuilding Scenes Frame by Frame

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If you’re working on molecular animations and tired of manually rebuilding scenes for every step, you’re not alone. Many molecular modelers struggle with creating smooth, reproducible animations that clearly communicate structural transformations or molecular motions over time. One recurring pain:…

A Simple Way to Select Atoms with Mathematical Precision

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Selecting specific atoms in large molecular systems can be time-consuming and error-prone—especially when working with complex structures like proteins, nucleic acids, or crystalline materials. If you’re a molecular modeler frustrated with manual selection tools or the limited filtering options in…

Protein folding in minutes: AlphaFold-2 predictions in SAMSON

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Predicting protein structures has long been a time-consuming challenge. Even with the advent of deep learning models like AlphaFold-2, integrating such powerful algorithms into your workflow can feel daunting. But what if you could launch an AlphaFold-2 structure prediction directly…

Precisely Orient Molecular Fragments in SAMSON for Cleaner Models

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When building molecular systems, precise positioning of fragments can make or break your simulations. Whether you’re assembling a drug molecule using building blocks or tweaking the conformation of a ligand bound to a receptor, intuitive control over fragment orientation avoids…

Improving Ligand Unbinding Pathways with P-NEB in SAMSON

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For molecular modelers working with complex ligand-protein interactions, understanding unbinding processes often means exploring energy landscapes – and that usually includes optimizing transition paths. This is where SAMSON’s Parallel Nudged Elastic Band (P-NEB) app comes in. If you’ve generated unbinding…

Easily Animate Atomic Movement with Keyframes in SAMSON

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Molecular modelers sometimes need to visually represent atomic motion in custom ways—for simulations, presentations, or educational purposes. But creating smooth, controllable animations without writing code can be a challenge. This is where SAMSON’s Move atoms animation comes in handy. If…

When Molecules Break Free: How to Easily Animate Undocking Events in SAMSON

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One common challenge for molecular modelers, structural biologists, and those preparing scientific presentations is communicating movement in molecular systems. Showing how a ligand detaches from a receptor, for example, is not only useful for storytelling but also enhances understanding of…

Zoom Without Distraction: Better Focus in Molecular Animations

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When creating scientific animations of molecular systems, clarity is key. A common challenge arises when trying to zoom in on a specific region of a molecule without inadvertently shifting the viewing target. This can lead to distracting camera movements that…