OneAngstrom – Page 112

Building Your Own Tools in SAMSON: A Practical Overview of Extension Development

When working in molecular modeling, it’s not uncommon to bump into limitations: maybe you want to use a specialized algorithm you published, or add support for a new file format, or even create a visualization style that better reflects your…

Making Molecular Animations Easier to Manage with Node Specification Language

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Creating and analyzing molecular animations is an essential part of many workflows in molecular modeling. Whether you’re visualizing conformational changes or simulating ligand docking, animations serve as a crucial step to understand dynamic phenomena. However, managing these animations directly in…

Fine-Tuning Colors in Structural Models: Exploring Custom Color Palettes in SAMSON

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Color can be a powerful tool when visualizing molecular systems, but choosing the right color palette is often underappreciated. For molecular modelers examining subtle variations in structure, properties, or dynamics, the difference between an adequate and a well-chosen color scheme…

Quickly Find Structural Groups by Atom Count in SAMSON

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When working on complex molecular models, a frequent challenge arises: how to quickly identify specific structural groups based on their composition—like groups with fewer than 10 carbon atoms or structures that exceed a certain atom count. If you’re spending too…

Filtering Side Chains by Atom Count in SAMSON with NSL

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In molecular modeling, especially in protein design and ligand optimization, analyzing and selecting specific parts of a molecule based on structural characteristics can save time and improve precision. One frequent task is identifying side chains with specific compositions, such as…

What if molecular modeling tools taught you how to use them?

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For molecular modelers who are just getting started—or returning after a break—one of the biggest time sinks can be just figuring out where and how to begin in a complex modeling platform. With so many features and specialized workflows, the…

Tracking Molecular Simulations in the Cloud: A Closer Look at SAMSON’s Job Manager

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Running cloud-based simulations can save significant time and local computing power, especially for molecular modelers working with resource-intensive tools like AlphaFold or GROMACS. But monitoring your jobs, accessing results, and maintaining an organized workflow across different simulations can quickly become…

Reusing Commands as Python Scripts in SAMSON

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One common challenge for molecular modelers using interactive platforms is the repetitive nature of certain tasks: adding hydrogens, applying color schemes, changing visual presets, and more. These actions, often done through graphical menus, can be tedious when applied regularly to…

No More Choppy Transitions: Animating Horizontal Camera Moves in SAMSON

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When working on molecular models, visual clarity can make or break your presentation. Whether you’re creating a high-impact animation for a paper, a conference, or a student lecture, smooth and intuitive camera transitions are essential. However, many molecular modelers struggle…

A Simple Way to Organize Complex Molecular Projects

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Working with molecular data often involves handling multiple structures, simulations, and associated files — all within a single modeling session. If you’ve ever felt overwhelmed navigating large molecular models or trying to apply the same operation to a group of…