OneAngstrom – Page 147

A Better Way to Navigate Your Molecular Scenes: Using Multiple Cameras in SAMSON

If you’ve ever worked on complex molecular systems, you’ve likely faced the challenge of jumping between different regions of interest. Whether you need a bird’s-eye view of the entire molecular complex or a close-up on a catalytic site, switching views…

Quickly Target Node Groups in SAMSON with the Node Specification Language

OneAngstrom

When working with large and complex molecular systems in SAMSON, finding and interacting with specific elements can become time-consuming. Imagine trying to select just the ligands, or isolate a set of residues from a cluster of chains, without accidentally selecting…

Modifying GROMACS parameters in SAMSON without breaking your workflow

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One of the recurring pain points for molecular modelers using GROMACS is managing and fine-tuning molecular dynamics parameters across simulations. Whether you’re running energy minimizations or full production MD simulations, adjusting .mdp files efficiently without making mistakes or interrupting your…

Working with Multiple Molecules in SAMSON: The Role of Document View

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Molecular modelers often juggle numerous molecules when working on simulations, analyses, or comparisons. Switching between them, copying structures, organizing data, and applying operations to specific groups without clutter can be a challenge. This is where Document View in SAMSON becomes…

Making Molecular Models Easier to Understand with Visual Models in SAMSON

OneAngstrom

For many molecular modelers, one significant challenge isn’t running simulations or optimizing structures—it’s presenting their results in a way that is easy to understand. Whether you’re working in research, education, or communication, visual clarity can save time, reduce misinterpretation, and…

Retaining Key Waters in Molecular Simulations: A Quick Guide

OneAngstrom

One common challenge in preparing biomolecular systems for simulation is managing water molecules. While bulk solvent can be added systematically during solvation, crystal waters—those resolved in the original structure—often have functional roles, especially around the active site of biomolecules. Automatically…

Make molecular slideshows clearer with background transitions

OneAngstrom

Presenting molecular models poses a common challenge: how to add clarity and context while keeping viewers focused on the important molecular features. Whether you’re preparing a lecture, pitching a research project, or creating a tutorial, one issue comes up frequently:…

What File Formats Does SAMSON Support, and Why Does It Matter?

OneAngstrom

When you’re working with molecular modeling software, one of the first real bottlenecks you might hit is file format compatibility. It often shows up when you try loading a structure you just downloaded from a public database—or even when trying…

Avoiding Common Pitfalls When Setting Ligand Atoms in Unbinding Pathway Simulations

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If you’ve ever tried to simulate ligand unbinding pathways from proteins, then you’ve likely faced the challenge of defining which atoms belong to the ligand — especially in systems containing cofactors, solvent molecules, or multiple ligands. Making a mistake at…

Effortlessly Track Atomic Motion in Your Presentations

OneAngstrom

When creating molecular animations or presentations, one of the recurring challenges for modelers is capturing the motion of atoms over time. Whether you’re simulating binding events, assembly steps, or conformational changes, showcasing how atoms move is essential—and being able to…