SAMSON Blog – Page 5

Quickly Select Chains Based on Structural Properties in SAMSON

One of the recurring tasks in molecular modeling is selecting specific parts of a model based on meaningful structural properties. When dealing with large or complex biomolecular assemblies in SAMSON, identifying chains with, for example, a specific number of residues…

Quickly Find Hidden or Locked Nodes in SAMSON Using NSL

OneAngstrom

Molecular modeling projects in SAMSON can involve highly complex systems, often made up of thousands of nodes: atoms, bonds, residues, visual models, and more. But what happens when you’re carefully inspecting your structure and something seems… missing? 🤔 Hidden or…

How to Efficiently Select Node Groups in SAMSON Using NSL

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When working with complex molecular systems in SAMSON, the ability to efficiently select specific parts of your model—especially node groups—is essential for organizing your workspace, automating repetitive tasks, or applying transformations and analyses only where intended. This post focuses on…

Capturing Atom Trajectories in SAMSON Presentations

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When building molecular animations or presentations, a common challenge is to visually track how atoms move over time. While SAMSON offers multiple ways to manipulate atomic positions — such as through simulation, docking, or manual movement — visualizing and saving…

Making Your Visual Models Work for You: Controlling Visibility in SAMSON

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When working on complex molecular systems, it’s common to feel overwhelmed by the sheer number of visual elements on the screen. Whether you’re analyzing a specific interaction site or preparing a figure for publication, being able to control which visual…

Running GROMACS Simulations in the Cloud Without Installing GROMACS

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For many molecular modelers, setting up a GROMACS simulation often starts with the same familiar workflow — downloading GROMACS, compiling it, troubleshooting library issues, and repeating the cycle on different machines or operating systems. It’s a time-consuming process that can…

Quickly Animate Atomic Motion Using Keyframes in SAMSON

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Creating effective molecular animations can be time-consuming, especially when you’re trying to convey subtle structural changes or transformations in a clear and controlled manner. Whether you’re preparing a scientific presentation or building an educational visualization, you’ve probably found yourself wrestling…

Speed Up Your Molecular Visualizations with Custom Visual Presets

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Creating clear and expressive molecular visualizations can be a time-consuming task. Whether you’re working on a presentation, preparing figures for publications, or simply exploring a structure, it often involves repetitive steps: selecting atoms, applying representations, choosing color schemes, adjusting views,…

A Simple Way to Show or Hide Molecular Visual Models in SAMSON

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When working on large molecular systems or complex scenes in SAMSON, keeping a tidy viewport is essential. Whether you’re publishing visuals, exploring specific subsystems, or simply reducing visual noise to concentrate on a specific interaction, the ability to quickly manage…

Placing a Lipid Layer Around a Protein Without Guesswork

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When setting up molecular dynamics simulations of membrane proteins, one of the most repetitive and error-prone steps is placing a lipid layer or bilayer around the protein. Aligning the protein, choosing the right lipid orientation, adjusting the box dimensions, and…