OneAngstrom – Page 17

Holding a Thought: Using Pause Animations in Molecular Presentations

When presenting complex molecular models, timing is everything. Whether you’re guiding students through a conformational change or highlighting a catalytic site in a biomolecule, viewers need time to absorb key visuals. This is where the Pause animation in SAMSON becomes…

Making Molecules Fade: A Simple Way to Show Structural Disappearance Over Time

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Visualizing molecular systems over time is a key aspect of effective scientific communication, especially when building presentations or educational material. One frequent need among molecular modelers is to illustrate the gradual disappearance of parts of a system—say, to focus attention…

Creating Multi-Walled Carbon Nanotubes in SAMSON: A Practical Guide for Molecular Modelers

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Building accurate models of carbon nanotubes (CNTs) for simulations or experimental planning can be time-consuming, especially when dealing with multi-walled configurations. For molecular modelers exploring structural, mechanical, or transport properties of CNT-based systems, being able to quickly generate these models…

Making Sense of Molecular Visibility in SAMSON: A Simple Guide to Presentation Flags

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When working with complex molecular systems in SAMSON, the molecular modeling platform, one common challenge is maintaining clarity in your scene. In large systems, certain parts often need to be hidden, grayed out, or emphasized for better understanding, analysis, or…

A Simple Way to Rotate Molecules Around Their Center

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When exploring and presenting molecular structures, visual clarity can make a significant difference. Molecular modelers and science communicators often need to rotate a molecule to showcase its shape, symmetry, or orientation relative to other molecules or fields. But executing this…

How to Minimize Only Part of a Molecule Without Affecting the Rest

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When fine-tuning molecular structures, one common challenge is minimizing only a subset of atoms without disturbing the rest of the system. This might be needed, for example, when adjusting a flexible loop in a protein or fixing a local geometry,…

Add Features to SAMSON Without Writing Code

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Molecular modelers often run into situations where a software tool feels limiting. You might want to visualize your data in a particular way, run a new kind of simulation, or open a specific file format, but your tools just don’t…

Running GROMACS Simulations in the Cloud with SAMSON: When Local Isn’t Enough

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Molecular simulations can be computationally intensive. Running extensive molecular dynamics (MD) simulations with GROMACS often requires significant local hardware resources, time, and configuration. This becomes a common bottleneck for researchers and students alike who need results but lack high-performance machines…

Quickly Find the Right Camera in Your Molecular Scene

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Managing complex molecular scenes can be time-consuming, especially when working with multiple cameras. If you’ve ever needed to select a specific camera—or a group of them—based on their name or state, you might have found yourself clicking around endlessly. Fortunately,…

Accelerate Fragment-Based Library Design with SMILES Manager in SAMSON

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Designing and optimizing molecular libraries can be a time-consuming and repetitive process, particularly when you need to generate compound variations by swapping out functional groups or fragments. If you’ve ever wanted to explore isosteric replacements or quickly prototype a series…