OneAngstrom – Page 151

Visualizing Ligand Unbinding with Pathlines: A Practical Guide

Studying ligand unbinding processes is a central task in computational drug discovery and enzyme mechanism analysis. However, tracking the motion of a ligand across a molecular dynamics trajectory can quickly become overwhelming, especially in complex systems with many degrees of…

Too Many Parameters, Too Little Time? A Simpler Way to Configure Your Production MD Simulation

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Setting up a molecular dynamics (MD) simulation is always a balance between precision and simplicity. When you’re preparing a production MD run—after carefully completing energy minimization and equilibration—you’re often faced with a long list of parameters that might feel overwhelming.…

Lock atoms in place during animations with SAMSON

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When working with molecular simulations or visualizations, there are times when you want part of the system to remain fixed—structurally intact—while the rest evolves or moves. For instance, you may want to animate the binding of a ligand while keeping…

Tired of File Format Errors? Here’s How SAMSON Makes Importing Molecular Data Easier

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One of the most common frustrations in molecular modeling is opening data files that just won’t load correctly. Whether it’s a Protein Data Bank (PDB) file with an edge-case formatting issue or an electron density map from a crystallography experiment,…

Making Molecules Disappear: Using the Hidden Animation in SAMSON

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When preparing molecular animations to communicate your findings—whether in academic presentations, lectures, or research videos—clarity is essential. A common challenge faced by molecular modelers is how to gradually remove part of a complex molecular structure without overwhelming visual transitions or…

Keeping Your Focus: Smooth Vertical Camera Moves in Molecular Animations

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When crafting molecular animations, it’s not just about what you show—it’s about how you show it. Whether you’re preparing an animation for a presentation, a publication, or simply to better understand a structure, precise camera movement can greatly impact how…

Running Molecular Dynamics in the Cloud with One Click

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Running molecular dynamics (MD) simulations using GROMACS often involves significant setup, hardware, and time. It’s not always easy for molecular modelers to configure local machines to handle large simulations, and setting up a remote compute environment can be daunting. The…

Quickly Filter and Find Render Presets in SAMSON with NSL

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When working with complex molecular models, scientists often face the tedious challenge of navigating and managing large numbers of visual elements—render presets being one of the most common components in scenes involving 3D views, materials, colors, and visual styles. If…

Need an Older Version of SAMSON? Here’s How to Install One

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Sometimes, sticking with a specific version of a software can be essential — whether for compatibility reasons, validated workflows, or teaching materials built around a particular layout. If you’re working with SAMSON, the integrative molecular design platform, the good news…

Quickly Space Out Complex Models: The Disassemble Animation in SAMSON

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Molecular modelers often face a familiar challenge: when working with intricate biomolecular assemblies or complex nanostructures, the sheer density of information in the model can make it hard to analyze or present specific parts. Whether you’re preparing a presentation, studying…