SAMSON Blog – Page 124

Why Your Molecule Looks Flat (And How to Fix It)

If you’ve ever struggled to make your molecular models look more three-dimensional, you’re not alone. Many molecular modelers face the same issue: molecules that should pop visually instead appear flat and lifeless. The culprit? Often, it’s the lack of ambient…

Finding the Right Molecule: How to Filter Molecular Structures by Attributes in SAMSON

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When working with complex molecular models, it’s common to end up with large systems composed of many different molecules, chains, residues, or even entire assemblies. Navigating this complexity can be time-consuming and error-prone, especially when your goal is to focus…

Quickly Selecting Cameras in Complex Molecular Models

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If you’re working with complex molecular scenes in SAMSON, you may have multiple cameras saved to record different views or prepare for rendering. Managing those cameras—especially selecting specific ones—can become tedious if you’re not using the Node Specification Language (NSL)…

Drawing Carbon Nanotubes with Your Mouse: A Quick Guide for Molecular Modelers

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For molecular modelers and nanoscientists, building custom carbon nanotube (CNT) systems often involves complex steps and scripting. Whether you’re exploring nanoelectromechanical systems or modeling drug delivery channels, getting the right geometry can seem like a slow start. If you’ve ever…

Filtering molecular folders by atom types and counts in SAMSON

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Working with large molecular systems often means dealing with folders that contain thousands—or even hundreds of thousands—of atoms. Extracting meaningful subsets of these data, such as finding folders with specific numbers of atoms, carbons, hydrogens, or residues, can quickly become…

Quickly Find Atoms by Element, Oxygenation, or Geometry in SAMSON

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In molecular modeling, it’s common to need specific subsets of atoms for tasks like analysis, visualization, or simulation. For example, you might want to display only the oxygen atoms in a protein, exclude hydrogens, or select planar aromatic carbons. Performing…

From Red to Green: Making Sense of NMR Restraints in Molecular Models

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One common challenge when working with NMR-derived molecular structures is ensuring that NOE distance restraints are actually satisfied in the resulting models. While tools for applying restraints exist, it’s often hard to see what’s going on—especially when dealing with multiple…

Running Python Scripts in SAMSON: What You Need to Know

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Many molecular modelers rely on scripting to streamline repetitive tasks and develop custom workflows. One common challenge, however, is finding a molecular modeling platform that allows direct execution of scripts — particularly Python scripts — without switching between environments. If…

Instant Molecular Beauty: A Guide to Visual Presets in SAMSON

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Communicating complex molecular systems often requires more than just structural accuracy—it demands clarity and readability. As a molecular modeler, you might spend valuable time adjusting colors, representations, and visual styles to produce a publication-ready image. What if you could do…

How to Define Reactive Sites for Analogue Generation Using SMARTS Patterns

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When designing new molecular analogues, chemists often wonder: Which part of the molecule should I modify to explore new activity profiles? In early-stage drug design, this is one of the most frequent roadblocks. If you’re interested in systematic molecular modification,…