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Quickly Highlight Reactive Sites in Molecules Using SMARTS Patterns

When working with small molecule design, one of the most common and tedious challenges is identifying chemical substructures you want to modify, replace, or expand upon. Whether you’re trying to explore structure-activity relationships (SAR) or optimize molecular properties, pinpointing the…

Freezing Motion: How to Hold Atoms Fixed Between Animation Frames in SAMSON

OneAngstrom

When preparing molecular animations, one common challenge faced by modelers is selectively immobilizing parts of a structure while letting others move. For example, you might want to show a ligand docking into a protein but keep the receptor rigid throughout…

From Sequence to Structure: A Quick Guide to Using AlphaFold-2 in SAMSON

OneAngstrom

Protein structure prediction is a critical challenge in molecular modeling. Whether you’re studying a novel enzyme, designing a therapeutic target, or working with systems biology models, knowing the precise structure of a protein is essential—but experimentally determining that structure can…

Mastering Node Group Selection in SAMSON: Simple Rules for Complex Models

OneAngstrom

When you’re deep into molecular modeling, every saved click counts. Whether you’re preparing structures for simulations, building hierarchical models, or just navigating complex systems, selecting the right node groups efficiently can streamline your workflow. In SAMSON, the Node Specification Language…

How to Create Smooth Molecular Zoom Effects with the Dolly Camera in SAMSON

OneAngstrom

One of the challenges in presenting molecular structures effectively is directing the viewer’s attention without disorienting them. Whether you’re preparing a research presentation, a teaching demo, or a visual summary for publication, showing transitions between different molecular views can make…

Keeping Your View Consistent When Animating in SAMSON

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When preparing animations in molecular modeling, maintaining a visually consistent perspective across frames is essential. Any unintended movement of the camera can lead to a jarring viewer experience or loss of focus on critical molecular features. This is a common…

Smoothly Rotate Molecular Structures Between Keyframes

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When preparing molecular animations for presentations or publication, one common challenge molecular modelers face is how to clearly convey spatial changes in the structure. Whether you’re assembling a trajectory, showing conformational changes, or simply rotating a protein for visual inspection,…

Making Molecular Models Disappear Smoothly: Controlling Visual Transparency in SAMSON

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When working with complex molecular systems, clarity and focus are often at odds. Molecular modelers frequently face challenges in presenting results in a way that highlights specific parts of the system without overwhelming the viewer. Whether you’re setting up a…

Quickly Filter Molecular Visuals with NSL Presentation Attributes

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When working with complex molecular models, molecular modelers often face the challenge of quickly locating specific visual representations—such as identifying what is and isn’t visible, or filtering only selected visual nodes. This process can get tedious when dealing with large…

Easily Apply Glass, Metal, or Emissive Materials in Molecular Renders

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One common challenge in molecular modeling is producing high-quality visuals that not only look good but also properly convey the nature of the materials involved. Whether you’re preparing images for publication, a presentation, or simply trying to better understand how…