SAMSON Blog – Page 6

Making Sense of Camera Selection in SAMSON’s Node Specification Language

When working with complex molecular models in SAMSON, many users take advantage of various node types such as atoms, bonds, groups, and cameras. Cameras play a key role in setting up and reproducing specific viewpoints or visual styles, which is…

Building Carbon Nanotubes by Hand: A Practical Workflow in SAMSON

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Designing carbon nanotubes manually can sound like a daunting challenge—but for molecular modelers needing custom nanotube topologies, it often becomes necessary. Whether you’re tweaking radii, optimizing ring positioning, or exploring non-standard conformations, having hands-on control over nanotube construction is essential.…

Controlling Note Visibility in Molecular Designs: A Simple Way to Stay Organized

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For researchers working with large molecular systems or complex models, visual clarity is critical. As projects grow, molecular modelers often annotate their systems using notes—whether to track hypotheses, mark interaction hotspots, or assist with collaborative storytelling. But as the number…

Quickly Select Chains Based on Structural Properties in SAMSON

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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

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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…