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Creating Multi-Walled Carbon Nanotubes: A Precise Approach with SAMSON

Structural precision is everything when you’re modeling at the nanoscale, especially when it comes to carbon nanotubes. Molecular modelers, materials scientists, and nanotechnologists often face the challenge of constructing multi-walled carbon nanotube (MWCNT) models with accurate geometrical parameters for simulations…

Clearer Molecular Visuals with Shadows, Silhouettes, and Depth: A SAMSON Preferences Guide

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One of the most common challenges molecular modelers face is understanding complex structures in 3D environments. Amidst crowded molecular scenes, it can be difficult to visually separate overlapping atoms or perceive spatial depth, leading to errors in interpretation or simply…

Getting Reliable Protein Predictions with AlphaFold-2 in SAMSON (and What You Might Miss Without It)

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Predicting protein structures is a recurring challenge for many molecular modelers, often involving complex workflows, heavy computation, and multiple configurations. AlphaFold-2 has revolutionized the field by improving the accuracy of protein structure predictions, but its integration in everyday modeling workflows…

Why Only One Editor Can Be Active at a Time in SAMSON

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As molecular modelers, we often switch between tasks — selecting atoms, deforming a structure, or building new models. In SAMSON, these diverse functionalities are accessible via editors. However, one design choice tends to raise questions: only one editor can be…

Why Your Extension Doesn’t Load in SAMSON (and How to Fix It)

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You’re excited to try out a new SAMSON Extension developed by your colleague—or maybe you’ve returned to your own favorite plugin after a break—only to see that it doesn’t load when SAMSON starts. 😕 This often confuses molecular modelers, especially…

Controlling What You See: A Guide to Molecular Model Visibility in SAMSON

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When working on complex molecular systems in SAMSON, clarity is key. With large assemblies, overlapping structures, and multiple representations, staying focused on relevant components can quickly become challenging. This is where understanding how to control the visibility of presentation nodes…

Quickly Finding Specific Files in SAMSON Using NSL

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When working on complex molecular systems, it’s not uncommon to accumulate dozens—or even hundreds—of structural and simulation files within a project. Finding those files manually in a crowded workspace can be tedious, especially when trying to isolate a specific conformation…

Progressively Hiding Atoms in Molecular Presentations: A Practical Guide

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When creating molecular animations, it often becomes necessary to shift focus, reduce visual noise, or reveal features step-by-step. Instead of abruptly switching views or hiding atoms instantly, a more refined approach is to progressively hide atoms and bonds over time.…

Dragging Atoms, Seeing Molecules React: A Closer Look at Interactive Simulation in SAMSON

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One of the most practical challenges in molecular modeling is verifying whether your molecular system behaves as expected during deformation — for example, when an atom is displaced from equilibrium. Traditional simulation setups often involve long preparation workflows and delayed…

Why Your Molecular Simulation Might Be Misbehaving (And How NPT Equilibration Helps)

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Have you ever run a simulation where the pressure never quite stabilizes? Or where your system density keeps drifting, despite starting from an apparently well-prepared structure? If so, you’re not alone. One of the trickiest aspects of preparing a molecular…