OneAngstrom – Page 1093

Using Your Own GROMACS in SAMSON Wizard: Why and How

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…

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

OneAngstrom

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…