OneAngstrom – Page 82

A Clearer View: Exploring Structures with Progressive Clipping in SAMSON

When molecular models get large and detailed, navigating and inspecting them in 3D can become visually overwhelming. Cluttered regions, overlapping atoms, or nested structures can make it hard to focus on specific internal areas of interest — especially in dense…

Exporting Ligand Trajectories from Path Simulations Without the Clutter

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When studying ligand exit pathways, molecular modelers often need a clean export of just the part of the system that matters: the ligand moving along its path. Exporting the full atom trajectories of an entire protein-ligand complex can quickly create…

Quickly Identify and Organize Labels in Your Molecular Models

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When working on complex molecular models, clarity is everything. Labels—whether for atoms, residues, or regions of interest—help molecular modelers keep track of critical information. But as models grow in size and complexity, managing these labels efficiently becomes crucial. That’s where…

Still Using the Wrong GROMACS Version?

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If you’re working with GROMACS for molecular dynamics simulations, there’s a good chance you’ve encountered compatibility issues between versions. Whether you’re trying to reproduce published results, align with your lab’s computing environment, or troubleshoot strange errors, using a specific version…

Working on Just One Part of a Molecule? Here’s How to Minimize It Without Moving the Rest

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When modeling large molecules or complex structures, it’s common to want to tweak and optimize just a small portion without affecting the rest of the system. Whether you’re refining the position of a side chain, adjusting a binding site, or…

Making Sense of Bond Types in SAMSON’s Node Specification Language (NSL)

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When working with complex molecular systems, identifying specific bond types quickly can save researchers a tremendous amount of time. Whether you are filtering for hydrogen bonds, distinguishing between aromatic or single bonds, or building precise molecular queries, defining correct bond…

Trouble stitching together WHAM results? Here’s a simpler way with GROMACS Wizard

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One of the recurring challenges molecular modelers face is extracting meaningful free energy profiles from umbrella sampling simulations. The workflow becomes particularly cumbersome at the post-processing stage — especially when dealing with tens or hundreds of windows, each producing individual…

From FASTA to 3D: Using AlphaFold-2 in SAMSON Without the Hassle

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For many molecular modelers, an all-too-common bottleneck is transforming a protein sequence into a reliable 3D structure. Whether you’re designing a new protein or studying the function of an uncharacterized one, waiting on complex installations or manually preparing jobs can…

Making Molecular Models More Readable with Ambient Occlusion

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One of the first challenges molecular modelers face when visualizing large and complex structures is how to make spatial relationships clear. Proteins overlap, structures twist around each other, and it’s easy to lose depth perception. A flat-looking model might look…

Animating Molecular Transitions with the Pulse Effect in SAMSON

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Creating clear molecular presentations often means finding the right balance between visual aesthetics and conveying scientific meaning. One common challenge many molecular modelers face is how to highlight specific structures or changes without overwhelming the viewer. Whether you’re preparing an…