OneAngstrom – Page 396

How to Quickly Filter Backbone Groups in SAMSON Using NSL

When working with complex molecular systems, identifying and manipulating specific backbone groups can quickly become overwhelming—especially in large biomolecular assemblies. If you’ve ever found yourself scrolling endlessly or zooming in and out to locate backbone components with a certain charge,…

Visualizing Bias: A Simple Way to Check Reaction Coordinate Coverage

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One common challenge in molecular simulations is determining whether you’ve sampled enough along the reaction coordinate during umbrella sampling. Incomplete coverage can lead to artifacts in the computed free energy profiles, making them unreliable. If you’ve ever spent days running…

Disappearing Labels? How to Control Label Visibility in Molecular Designs

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Have you ever zoomed into your molecular system in SAMSON and wondered where your carefully added labels went? Or perhaps you stepped back from a large complex and the labels cluttered the view? If you work with molecular models and…

Finding the Chains That Matter: Using NSL to Filter Molecular Chains by Attributes

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Molecular modelers often need to extract specific chains from complex molecular systems—chains with a particular number of residues, chains that are visible, chains that follow a naming convention, and more. Manually browsing through large biomolecular structures to find the right…

Choosing the Right Unit Cell for Efficient Molecular Simulations

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When setting up molecular dynamics simulations, especially in biological or materials science contexts, one often faces an overwhelming number of choices. One such choice that significantly impacts both simulation accuracy and performance is the shape of your unit cell used…

Optimizing molecular transition paths with P-NEB in SAMSON

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When simulating molecular mechanisms, such as how a ligand unbinds from a protein, researchers often face a specific challenge: known initial and final states of a system are available, but the energetically plausible path that connects them is not. This…

Drawing Carbon Nanotubes with Your Mouse: A Visual Approach to CNT Modeling

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Creating accurate carbon nanotube (CNT) models is a common yet often cumbersome task in molecular design and nanoscience. Whether you’re preparing nanostructures for simulation or designing nanoscale devices, defining geometry and chirality vectors manually can interrupt your workflow. But what…

Keeping Your Focus: Horizontal Camera Motion Made Easy in Molecular Animations

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When working on molecular presentations, particularly those involving systems like membranes, surfaces, or long assemblies (e.g., DNA or polymer chains), it’s often essential to maintain a consistent perspective while shifting the viewpoint across the structure. A common challenge arises: how…

Making Molecules Appear When It Matters: The ‘Show’ Animation in SAMSON

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When you’re preparing a molecular presentation, timing can make a big difference. Whether you’re explaining a protein-ligand interaction to colleagues, teaching a structural biology class, or preparing a video abstract for your next paper—how and when your molecules appear on-screen…

Sketching Molecules in an Integrated 2D-3D Environment

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For molecular modelers, quickly drafting, editing, and visualizing molecules often requires switching between tools—or between 2D and 3D views. This can lead to inconsistencies and disrupt the workflow. SAMSON’s Interaction Designer addresses this pain with a synchronized 2D-3D sketching environment…