OneAngstrom – Page 324

Quickly identify groups of atoms in SAMSON using selection attributes

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…

How to Quickly Find Hidden or Visible Nodes in Molecular Scenes

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When working on large molecular models, it becomes increasingly important to manage visibility efficiently. You might be focused on just one part of the structure — a ligand binding site, a water shell, or a specific chain. But if hidden…

Efficiently Filter Charged Residues in SAMSON with NSL

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When working on protein modeling workflows, one of the recurring tasks is identifying and selecting residues based on their electrical charge. Whether you’re optimizing electrostatic interactions, analyzing salt bridges, or preparing electrostatics-related simulations, filtering charged amino acids is a crucial…

A Step-by-Step Guide to Building Custom Molecules Atom by Atom in SAMSON

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Molecular modelers frequently need to construct specific chemical structures not readily available in molecular libraries. Whether you’re reproducing a model from a journal article or exploring new chemical scaffolds, building molecules atom by atom is often a key part of…

Easier Custom Atom Selection in GROMACS Simulations with SAMSON

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Many molecular modelers using GROMACS have run into this: you want to track or manipulate a specific set of atoms during a simulation—maybe the side chains of neutral amino acids or every non-C-alpha atom in a protein. But GROMACS only…