OneAngstrom – Page 227

Easily Center and Align Your Molecules in SAMSON

When working with molecular models, even small inconveniences in object positioning can slow down your workflow. Whether you’re preparing figures for publications, aligning structures for simulations, or simply organizing your workspace, having molecules scattered arbitrarily in 3D space can be…

Getting More Control Over Polymer Sequences in Molecular Design

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When designing complex polymer structures, one common challenge for molecular modelers is efficiently defining and managing sequences of monomer units. Particularly in synthetic or biopolymer design, having both precision and flexibility in how monomers are arranged is crucial for building…

How to Focus on Meaningful Molecular Segments Using NSL Filters

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When you’re working with complex molecular systems, identifying the right segment to analyze or visualize in your workspace can be a challenge. The sheer number of atoms, residues, and structural groups in large biochemical systems can be overwhelming. This is…

Making Sense of Visible, Hidden, and Flags in Molecular Scenes

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When working on complex molecular systems, clarity is essential. A major pain point for molecular modelers is managing the visibility of objects within a scene—especially when you’re juggling dozens (or hundreds) of nodes, each with specific visual properties. Why is…

Vertical Focus: Making Better Molecular Views with the Pedestal Camera in SAMSON

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When building presentations or visualizing complex molecular systems, molecular modelers often face the challenge of clearly highlighting vertical structures—think membrane-spanning proteins or stacks of molecular layers. A static camera angle can miss these intricate features, while overly complex animations may…

Quickly Highlight Reactive Sites in Molecules Using SMARTS Patterns

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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

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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

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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

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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

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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…