OneAngstrom – Page 572

Watching the SARS-CoV-2 Spike in Motion: A Tool for Molecular Designers

Understanding the dynamics of biological macromolecules like proteins is crucial for many molecular modeling applications, from drug design to structural biology. One common pain point? Visualizing and simulating conformational transitions between different functional states of a protein — especially when…

A Simple Way to Create Custom GROMACS Index Groups in SAMSON

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For many molecular modelers working with GROMACS, defining custom index groups is a familiar but often tedious task. Whether you’re preparing complex systems or performing steered molecular dynamics, accurate grouping of atoms, residues, or chains is essential. One particularly common…

Avoiding Common Pitfalls When Adding Ions to Coarse-Grained Systems in GROMACS Wizard

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When preparing coarse-grained (CG) molecular systems for molecular dynamics (MD) simulations, one crucial step is the addition of ions. This step ensures charge neutrality and mimics physiological conditions. However, it’s easy to encounter unexpected issues—especially when working with CG models—if…

Installing Python Packages in SAMSON: A Quick and Flexible Workflow

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Whether you’re analyzing molecular dynamics, building neural network models for protein folding, or integrating your own Python toolkits, managing your Python packages efficiently is essential. Unfortunately, for many computational scientists, package installation can be frustrating. Switching between environments, worrying about…

Controlling Molecule Visibility in SAMSON with NSL Filters

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When working with complex molecular systems, it’s easy to lose track of what’s visible in your scene and what isn’t. Whether you’re analyzing a macromolecule, building simulation-ready models, or preparing visuals, controlling what shows up on screen can make a…

Filtering Side Chains by Atom Composition in SAMSON

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One of the most common challenges in molecular modeling is quickly identifying specific side chains based on their chemical properties. Whether you’re performing structure refinement, dataset curation, or preparing inputs for simulations, being able to filter out side chains based…

Better Molecular Scenes with Visual Presets in SAMSON

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Molecular modeling often involves balancing scientific accuracy with visual clarity. Whether you’re preparing molecular graphics for a publication, presentation, or educational material, achieving visual consistency while highlighting important features can be time-consuming. This is where SAMSON’s Visual Presets come in.…

Tired of Atom Jumps in Molecular Animations? Keyframes Can Help

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When preparing a molecular animation, it’s easy to face one frustrating issue: unnatural atomic jumps from one frame to the next. Whether you’re presenting a conformation transition, simulating a nanotube breathing cycle, or demonstrating ring flipping, discontinuous movement can make…

Editing Molecular Properties in SAMSON: A Closer Look at the Inspector

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When working with complex molecular systems, fine-tuning details like atom charges, bond orders, or node visibility is a common yet often tedious part of the modeling process. For many molecular modelers, the challenge is not just building a structure, but…

A Better Way to Pan Molecular Systems Horizontally

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When creating molecular animations, clarity in how structures are presented is crucial. Whether you’re preparing content for a paper, a teaching video, or a presentation, it’s often necessary to move the camera horizontally—especially when showing large assemblies or when comparing…