OneAngstrom – Page 622

From Concept to CNT: A Simple Way to Build Carbon Nanotubes in 3D

When modeling at the nanoscale, researchers, educators, and engineers often need to quickly generate accurate carbon nanotube (CNT) structures. Whether you’re simulating molecular transport, designing nanoelectromechanical systems, or visualizing nanoscale materials, building CNTs manually can become repetitive and error-prone. The…

Controlling Visibility in Molecular Presentations Without Tweaking Transparency

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Molecular animations can quickly become overwhelming when dealing with complex structures, especially when multiple elements appear and disappear during a presentation or simulation. A frequent challenge for molecular modelers is ensuring clarity in dynamic visualizations: how do you focus attention…

Using Your Own GROMACS in SAMSON Wizard: Why and How

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Many molecular modelers rely on the GROMACS engine for performing complex molecular dynamics simulations. While using the default versions bundled with visualization platforms is convenient, there are valid reasons to switch to a custom GROMACS version for local jobs. Whether…

Tracking Moving Molecules: Let the Camera Follow Your Atoms Automatically

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When studying the dynamics of complex molecular systems, one of the challenges modelers often face is visual clarity: how to keep visual focus on specific atoms or molecular fragments as they move throughout a simulation. If you’ve ever found yourself…

Quickly identify groups of atoms in SAMSON using selection attributes

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Molecular modelers often work with very complex systems, frequently involving large biomolecules, materials, or supramolecular assemblies. Navigating these models efficiently often depends on the ability to select and manipulate parts of the system based on their structural or logical organization.…

Adding a Lipid Layer Around a Protein without Headaches

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Setting up lipid membranes around proteins can be a time-consuming and error-prone task in molecular modeling workflows. If you’ve ever tried to manually create lipid bilayers and fit them around membrane proteins, you know how tricky it can get—from orientation…

FASTA in, Structure out: Using AlphaFold-2 in SAMSON

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Many molecular modelers face a common challenge: how to obtain reliable 3D structures for proteins when experimental data isn’t available. Whether you’re trying to model a newly discovered sequence or understand domain interactions, structure prediction is your go-to route. Fortunately,…

A Simple Way to Stay Organized When Modeling Molecules

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If you’ve worked on large or multi-step molecular modeling projects, you’ve probably faced the challenge of managing complex structures, reference files, scripts, and various annotations — all within a single workspace. Managing molecular data can quickly become overwhelming when everything…

Choosing the Right Discrete Color Palette for Molecular Visualization

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When you’re building complex molecular models, visuals matter. Whether it’s distinguishing between different protein chains, highlighting interaction sites, or simply making your work look more readable and aesthetically pleasing, choosing the right color palette can make a big difference. Color…

Easily Control Molecular Visibility with the Shown Animation

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When creating molecular animations for presentations, publications, or educational videos, one of the simplest but often underestimated challenges is managing which elements of the model the audience sees — and when. If you’ve ever wanted to reveal specific molecules or…