Uncategorized – Page 357

Making Molecular Projects Self-Contained with Embedded Files in SAMSON

One common frustration when collaborating on molecular design projects is making sure all files stay together — simulation outputs, analysis scripts, papers, images, and custom data often need to be manually tracked and bundled when sharing or switching between machines.…

A Simple Way to Reveal Atoms Over Time in Molecular Animations

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Creating effective molecular animations can be tricky, especially when you want to illustrate how a molecule becomes structured, how atoms bond progressively, or how a system transitions from disorder to order over time. One frequent challenge is controlling the visibility…

Adding and Removing Modules in SAMSON Without the Guesswork

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For many molecular modelers and scientists, customizing your molecular design environment is essential. Whether you’re simulating proteins, docking ligands, or running cloud-based structure predictions, adapting your tools to fit your workflow is critical. That’s where SAMSON Extensions come into play.…

Switching Views Instantly in Molecular Models

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When working with complex molecular structures, modelers often need to switch between multiple viewpoints quickly — zooming into a binding site, looking at an overall protein fold, or comparing two conformations side-by-side. This can become time-consuming and repetitive if you…

Avoid Solvent Clashes in Martini Simulations with This One Setting

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When working with coarse-grained (CG) systems in GROMACS using the MARTINI force field, one recurring issue for molecular modelers is solvent bead clashes during solvation. These can lead to non-physical behavior during energy minimization or even cause simulations to crash.…

How to Select Atoms by Expression Without Writing Scripts

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For molecular modelers working with large systems, it’s common to face repetitive and time-consuming tasks like selecting specific atoms based on custom values, geometric patterns, or chemical types. Doing so manually through the interface—especially over thousands of atoms—can become tedious…

Quickly Filter Visible Labels with NSL in SAMSON

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When working on complex molecular systems in SAMSON, labels can be critical for clarity — but too many of them can clutter your visualization. Molecular modelers often face the challenge of managing these label nodes efficiently, especially when preparing clean…

What Are Node Types in SAMSON (and Why Should You Care?)

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Anyone working in molecular modeling or structural biology knows that dealing with complex systems often means juggling different layers of information: atomic coordinates, chemical bonds, visual styles, simulation data, annotations, and more. If this sounds familiar, you may be relieved…

Why Only One Editor Can Be Active at a Time in SAMSON

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When working with complex molecular models, workflows can often become tangled—especially when juggling multiple tools. If you’ve ever wondered why SAMSON, the molecular design platform, allows only one editor to be active at a time, you’re not alone. This design…

Switching to Your Own GROMACS: When and How to Do It in SAMSON

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If you use GROMACS frequently for molecular dynamics simulations, you’re probably familiar with situations where you need to run simulations with a specific version of GROMACS — for example, for reproducibility in publications, for performance comparisons, or simply because your…