OneAngstrom – Page 175

How to Quickly Select and Organize Light Sources in Your Molecular Scene

When building a molecular scene in SAMSON, lighting plays a key role in making sure that your visualizations are both scientifically clear and aesthetically compelling. But if your project involves multiple light nodes—think of directional lights, spotlights, or ambient light…

Choosing the Right Color Palette in Molecular Visualization

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Color can be more than visual appeal when modeling molecules—it communicates information, separates regions, and reveals trends. But choosing a color palette that fits your goals can be difficult, especially when you want clarity across complex molecular assemblies. If you’re…

An Easier Way to Work with Residue Selections Across Views

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When analyzing biomolecular structures, a common frustration is keeping selections consistent across different representations of your model. If you select a residue or chain in a 3D viewport, it can be tedious to track it back to its sequence position—or…

No GROMACS Install? No Problem.

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Installing GROMACS for molecular modeling and simulation has traditionally been a technical barrier for many researchers and students. It often involves downloading source code, managing dependencies, ensuring compatibility with specific compilers, and sometimes taking deep dives into system-level settings. If…

Controlling Visibility and Selection in Molecular Models with NSL

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Working with large molecular systems often means dealing with a lot of visual clutter. Whether you’re preparing illustrations for a paper or simply trying to understand a structure better, it’s common to want to hide some elements and highlight others.…

A More Precise Way to Select Node Groups in SAMSON

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When you’re working with complex molecular systems in SAMSON, quickly finding and editing specific parts of your model can be challenging — especially when your structure involves large biomolecules, molecular assemblies, or nested node groups. Fortunately, SAMSON’s Node Specification Language…

Quickly Visualize Symmetric Protein Assemblies from PDB Files

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If you’ve ever loaded a PDB file into your molecular modeling environment only to find a lone asymmetric unit floating in empty space, you’re not alone. Most PDB files describe just the minimal repeating unit of a biological assembly or…

Getting the Right Molecular Selection with Selection Filters in SAMSON

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When working on complex molecular systems, the ability to quickly select relevant atoms, residues, or molecules is vital. Whether you’re visualizing a protein-ligand interaction, preparing a simulation, or analyzing channels through a membrane, making precise selections can save time and…

Selective Visibility in Molecular Models: A Simple Way to Focus on What Matters

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Molecular modelers often face a common challenge: navigating through visually complex structures to focus on specific parts of interest. Whether you are preparing figures for presentations, examining a ligand-binding site, or trying to identify specific substructures, controlling what is visible—and…

From Trajectory to Insight: Selecting Initial Conformations for Umbrella Sampling in SAMSON

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Molecular simulations often rely on enhanced sampling techniques to capture rare events or transitions. One such method is Umbrella Sampling, widely used to estimate free energy profiles along reaction coordinates. However, a common challenge many molecular modelers face is determining…